I'll take care of your dog.

Where do ya live?
Seriously, I've traveled A LOT with my Basset Hound. You'll do just fine finding hotels, especially because your fur-baby is so small. The hotel management starts to get a bit nervous when you say you have a 70-pounder (or above.) And their first question seems to almost always be "what breed?" -- ostensibly because they want to gauge the Potential Bark Factor. This was my first experience with Basset Discrimination, by the way.

. Most hotels/motels say you can't leave the dog unattended in the room. But some don't. You'll also find that you'll have to pay a "pet fee" probably.
Then again, my Dad and I used to *sneak* (yeah, right) our 90-pound Golden Retriever into hotels every summer when we drove cross country. MOTELS are actually best for this...the ones like Holiday Inn that have all sorts of seperate guest entrances. Then again, your dog is so small, sneaking her in shouldn't be a problem.
Also, I've found that a lot of touristy places have kennel facilities -- when we were at Carlsbad Caverns in NM, my pooch had a very nice 3 hour nap in a cozy kennel with a/c. And on the topic of NM...my dog was even allowed in a TAXI in Santa Fe (and in a restaurant), so maybe it's just a New Mexico thing.
There are tons of books out there about where to stay with you pet, so you can pretty much plan out where you're going to stay beforehand. And as for what to do with her when you can't be with her...I like the doggy daycare idea. And not just because I WORK at one, either.

Check online to see if there are any in the area where you're going. It's a HUGE growth business, so you might be surprised by how many you find. I know you said she has special needs, so you could call ahead and ask how they would deal with those (or if they would). We have a diabetic Daschund where I work and I do insulin shots for him, so you never know what they'll say. Also, maybe you could check out actual kennels in the area and ask if she could just stay for the day or whatever. That might be better than daycare for her if she's nervous around other dogs, etc.
That's all my wisdom. I could give you some advice on how to travel cross-country with 2 cats, too. That advice would be: DON'T.

Worst 5 days of my LIFE. And my Basset has traveled trans-Atlantic, too.

. But I won't bore you with that story.
Good luck and have fun!