Things that Have Not Changed
Trusting your players is Crucial
This is likely to be easier for you, as a freeform player used to using only trust and social contract to decide what happens in the game, than for many long-time players of rules-heavy systems: the rules do not protect you from abusive players, and you must trust your players just as much with a rules-heavy system as for a freeform game.
Note that even for well-meaning players, the rules can seem to give license to various things that can ruin your game – and also that unless the group talks about what they want and expect from the game, it’s unclear what rules can be counted on to be in effect and reliable for basing a character’s power upon, and which rules technically allow actions you do not want or are too much for your game.
Your players must trust you
This hasn’t changed either. Particularly since you are new to the system, and you cannot stop the game to look up a rule all the time, you’re going to have to make uninformed decisions about various rulings. Wherever possible, build upon this trust by trusting your players, and allowing their interpretations (at least until you sit down and read the rule yourself, after the game), so that you can, when necessary, choose to rule against them.
Story, plot, tone, and characterization remain king
All the skills you have from freeform roleplaying will serve you very well DMing a rules-heavy game. These skills are the things that bring the rules to life and make the game worth playing. It’s important for you to know that these things remain just as important; don’t assume that just because you’re playing a rules-heavy game, you need to make the game about the rules. The rules are there only to facilitate play.
Things that Have Changed
The rules dictate a lot of the setting
Playing Dungeons & Dragons or Pathfinder means you have a lot of rules for things like stabbing a goblin in new and interesting ways, looting long-lost tombs of their mysterious wonders for fun and profit, and so on, but quite a few less rules, and less detailed rules, for things like setting up a bakery, courting the princess, or piloting a starship. The books describe the societies of elves and orcs and humans and halflings in great detail, but not so much how any of them would handle outer-space colonies (well, at least in the default material; Dungeons & Dragons did have the Spelljammer setting in 2e) or an industrial revolution (though again, you could use Eberron for that).
Your choice of system constrains the sort of game you can play. Dungeons & Dragons tries to be fairly generalist (though I’d claim that they assert far more generalization than they actually offer), but ultimately it is high-magic, fairly high-power, and very much about fantastical adventures. While it can be forced to play other sorts of games, and even handles some variations pretty well, there are usually other systems designed with other priorities in mind that may handle a different sort of game better than Dungeons & Dragons would.
Your players have to rely on the rules to accomplish things
The actions available to your players are listed in the books, with associated action costs, resource usages, and so on. While they can (and should) come to you to discuss how to handle actions not discussed in the rules, or that maybe the rule here is a bit too punitive for someone who should be good at something (or, on the flip side, how the rules make something difficult a bit too easy, though only very honest players are likely to bring that up), they cannot, under the rules, make those decisions for themselves.
The significance of this, for you, is that you have to allow the rules to function in some fashion or another. If none of the rules function as written, then the players are not able to do anything reliably and won’t know how to take their turns. You can, of course, replace any rules you like (the so-called Rule 0), but if you find yourself doing it a lot, then that may be a sign that you should look for a different system.
So you need to get used to the idea, particularly with players with more system mastery than you, that they are going to do things you didn’t realize they could, and maybe you wouldn’t have thought they should be able to do. You will, at times, need to choose to change the rule; the rules are not perfect. But you have to bear in mind the limitations that the players are under, and make sure any ruling you make is for the good of the game. If someone’s abusing a cheap rule and it’s ruining the game, you have to change it. If someone does something unexpected, and it wipes out the supposedly-tough boss way more easily than you expected, eh. It’s a learning experience and gives the player a chance to be awesome. You just have to keep in mind that a balance between these two things is necessary.
You are also somewhat limited
You have the authority to add, remove, or change any rule in the game, but ultimately the system only works well if you’re actually using it. Thus, while you definitely should make changes as necessary to accomplish the game you want, you should probably think about your new rules in terms of fitting them into the system as a whole. If you want to add a new ability for characters who have no magic at all to throw off magical effects, you need to figure out if that’s going to be a Saving Throw or a Skill Check, or whatever else, what the DC is, how often they can do that, etc.
You will have to read and learn
This kind of goes without saying, but it is new, and it is important: to use a system, you need to know its rules. You do not, however, have to know every nitty-gritty detail. Remember: trust your players, and expect them to trust you. Trust them to know how their characters work, and expect them to trust you when you tell them that no, at least until you get to know the rule better, you’re not going to allow that to work quite that way. Focus on the basic rules, and know those, and have a general gist of how the players’ abilities work (“OK, so he trips a lot, so expect guys to get knocked down a lot,” and “she casts spells, so she’ll have a big effect on things every now and then, but she only can a few times per day”), but otherwise just run with things. It’s the only way to really learn, at the end of the day.
As a DM, rather than just another player in a group freeform RPG, you need to think about the entire world around the players, and that means knowing who they’re going to see, and if you expect them to fight any of these characters or monsters, what they can do. You should not try to learn the entire system at once, but rather learn the rules relevant to each encounter and in that way gradually build up knowledge of the system.
To this end, look around online; it can be a fantastic source of information on the system. Unfortunately, with Wizards’ recent reformat of their message boards, finding a lot of the old information about 3.5 is very difficult, but you can. There are also numerous other boards. You can much more quickly learn the system by reading tutorials, articles, and the like than by trying to read through all the rules and synthesize the conclusions yourself (you do, of course, also have to go back and read the rules).
And take advantage of talking with other, more experienced players: you can join us in the Chat, or in another D&D chatroom (I spend a lot of time in #giantitp for example) for help, but it might be even better if you know someone with skill levels and experiences similar to your players, but not playing the game. Or you could really go all-in on Number One, and get your players to help build enemies (this will potentially ruin a lot of surprise, though, unless you get creative with how you spring them on the players suddenly when they aren’t expecting that thing).