I'm fairly new, but I'll answer...
1) What's the deal with the skull and crossbones on the cute clothes for the furbabies? Is it a logo or brand thing? I've liked some of the clothes but didn't purchase because the skull and crossbones just didn't seem to match the innocence of a Yorkie's face.
I look pretty innocent and I love skull clothing (even have some in my tattoos). 
I had Darlin Bows custom make me the cutestttt little pink and black bow with a skull on it. Missy hasn't worn it yet, but when she does I will take a pic. We all have our own interpretation of what's "cute". 
2) If any of you use the cute little caps and
[COLOR=green! important][COLOR=green! important]hats[/COLOR][/COLOR]
http://kona.kontera.com/javascript/l...rey_loader.gif , how was the experience of first putting them on? Do you think it hurts the ears? I don't like them.
Missy has a hood on her jacket, but I usually fold it down unless it's raining. I'm not fond of caps and hats either.
3) What on earth is a Yorkie-poo? Is that a term of endearment or a
[COLOR=green! important][COLOR=green! important]bathroom[/COLOR][/COLOR]
http://kona.kontera.com/javascript/l...rey_loader.gif accident?
Haha, a cross breed of a Yorkie with a Poodle.
4) What are the doggie
[COLOR=green! important][COLOR=green! important]colognes[/COLOR][/COLOR]
http://kona.kontera.com/javascript/l...rey_loader.gif ? I mean I certainly know what cologne is but why would you slosh some on your Yorkie? Maybe I'm missing something here.
I'd rather my dog just smell clean from a bath.
5) When we take possession of our
[COLOR=green! important][COLOR=green! important]puppy[/COLOR][/COLOR], we will then face a 7-hour drive home. We debated about getting a room halfway home but I thought it would be best to reach the house to help the puppy rest. (I know...there's probably going to be no rest...LOL) Is my thinking a mistake here? One consideration is getting home in daylight but we will be able to.
I'd head straight home, but that's just me.
6) I think I've gotten almost everything imaginable for her and I've made her wellness appointment with the vet. I've also checked into the starting dates of the next puppy classes but haven't actually signed her up. Is there anything else I need to do?
Well, if you have "everything imaginable" then you must have all bases covered 
7) Do you take water with you on your walks for your Yorkie? I've bought a gadget that resembles a water bottle but she can "drink" as dogs do but I don't know if it's really necessary.
Missy doesn't walk very far yet, but I wouldn't bother with the water. Unless we're going to be out and about for quite awhile.
8) Also, I bought some of the cutest, tiniest bows I've ever seen! When should I start using them or how will I know when to start?
I'm just starting now, and Missy's 21 weeks.
9) Same thing about the clothes...when should I start with them? Should she be a certain age or should I start while she's still adjusting to her new home so she'll just think it's another weird thing here. She's mainly only going to wear them on walks, etc.
I started Missy wearing clothes (sock sweaters) as soon as I got her, only because she gets cold! She loves wearing clothes.
10) If I'm the one that does all the upkeep on her...will she associate me with the things she's not particularly fond of?
I always give a treat after grooming, nails, bath etc. At first, I started with a few treats then cut it back over time as she relaxed with everything. If you do this, your pup will associate "upkeep" with something positive. It's working great for us. Missy went from hating being brushed, teeth brushed, nails cut...to loving it. I brainwashed her with treats 