I second everything AceCalhoon said and he said it better than I could.
But I think I can add a couple of relevant things.
I use the rulebooks for inspiration and modify relentlessly
Personally, I think homebrew has a lot of advantages. It lets the GM have more creative control, and lets the GM tailor the rules to his group and his situation.
Also, your players if they have been playing for a while are probably expert in the monsters in the Monster Manual. But a group of first level characters shouldn't be. One way to help ensure that the players have some surprises is to only use the manuals as a rough guide.
You need to communicate clearly that it is homebrew.
AceCalhoon said this, but I think it is worth emphasizing. When I GM, I always take lots of liberties with the rules and the monsters especially. But, I always make sure my players know that before they so much as make their characters.
Failing to explain ahead of time can lead to frustrated and angry players as they repeatedly get surprised in ways they did not expect to be surprised. On the other hand, if they expect to encounter variations ahead of time then it becomes a possibly interesting new dynamic. It encourages them to do in game research (really talking to the survivors of the last attack instead of just hearing "dragon with red scales" and rushing off to get fire-protectiong), and it encourages them to fight cautiously, ready for the monster to break out an unexpected ability.
Be ready to adjust
While certainly not perfect, most premade settings have a decent amount of verisimilitude. You of course can achieve the same or better, but that takes a lot of work. So, if one of my players points out something that really challenges the verisimilitude in a reasonable way, I always stand ready to either make up an ad-hoc explanation or even go back and change my plans.
What I mean is that if a player says something like, "But that is from Krynn and this one is from Faerun", then that doesn't really challenge the verisimilitude but highlights my deviation. I blithely respond, "And this is neither, but inspired by both."
But if a player says, to borrow from AceCalhoon's answer, "How are the Dogeaters and puppylovers living in peace?" I will try to come up with a reason or else say something like, "Did I say puppylovers? I meant kittylovers..."
It depends on playstyle
Again, AceCalhoon touched on this, but playstyle matters a lot. I'm sure its obvious from this answer I prefer a more narrative style with emphasis on plot, exploration, and discovery. By going homebrew, I can make more things to discover and tailor everything to the plot.
If you want a very tactical game, you probably do want the players to really know the exact abilities of everything they encounter. In that case, it might make more sense to stick with the manuals or else be very open, explicit, and upfront with the changes prior to the fight.