Protection against Spells
Disguise Undead (from the Spell Compendium) does just what it says - hides undead. Unfortunately Clerics can't cast it, so you'll either need an Arcane casting lackey to do it for you, or an item that can do it (Wands with Use Magic Device, or some other use per day item).
Undetectable Alignment can hide the alignment of one creature per casting for 24 hours from all forms of divination (including the detect spells). That doesn't make them look not-Undead, of course, it just means that detect spells and the like will fail to see their alignment.
False Vision can create a fake image if someone uses Scry on you, so they see what you want to see. You'll need the Trickery Domain to cast it, though. Pretty useful if you retreat somewhere private to create more undead minions or heal the ones you have, as you don't want someone spying on you doing that and giving away the secret.
Magic Aura lets you change or hide the aura on creatures, so someone looking at auras wouldn't notice the other stuff you cast on your Undead. This requires the Magic Domain to cast. Of course if they have masterwork full plate, you could just claim the armor is magic and that'd explain the aura. A good Bluff will help that.
Protection against Spot
You'll want a disguise so that someone just casually looking around doesn't notice that you have Undead with you. Ideally, they'd be mistaken for guards. You mentioned full plate, which if it's totally obscuring of the features of the Undead, might work okay.
A Hat of Disguise would help quite a lot, as it gives +10 to a Disguise check and Disguise says that casual observers don't even get a check to notice you while using it (you'd have to draw attention or interact with them somehow). That should let you walk through a town more or less freely so long as you don't draw attention to yourself. It'd get expensive to outfit a lot of Undead with it, though.
You can use Disguise without the hat, but the check results won't be that great as most Undead don't have ranks in it. Or if you have a good disguise score yourself, create the disguises for your undead. That will take a very long time if you have several of them.
Protection against Scent
Scent is a tricky one, for creatures that have it. Theoretically Disguise Undead or Disguise Self might work as mentioned above, as they don't say that they don't (they mention audio and tactile senses as ones that aren't fooled, so you could argue that they can alter scent). I'm honestly not sure if they do or not.
Remove Scent (Spell Compendium) can also remove scent for a short time, but once again it's not a Cleric spell.
Fortunately, in general there's no special rule that says Undead waking by will scare animals off just by smell, so you may not have to worry a lot if your other disguises work.
If you're going somewhere for a while that you don't want your guards around because you can't hide them from the people in the area, use a Portable Hole or a Bag of Holding. So long as you don't have so many Undead that they don't fit, they can stay in there forever, until it's safe for you to bring them out. If someone asks, you sent your guards off for a time for make up some lie.