1. I live in a townhouse, so I have stairs in my home. Should I keep my puppy in a most of the time to avoid it getting hurt on the stairs? I'm guessing it may be a good idea to keep it in the pen in general for a while. Any certain age when I could stop?
In my experience- pups dont bother trying to get upstairs untill they are confident- they look daunting to dogs. I think a stairgate might be the best option- or leave it to roam free in a room that doesnt have access to the stairs whilst you are up there
2. I have three cats. Would the puppy do ok with them for the most part? The cats like to tackle each other, but none are overly aggressive. None have ever been around a dog before.
Having only ever socialised dogs with my tortoises, I would say, have a small meeting, and dont force the cats and dog to be in the same room, and dont make a big fuss of either- just act as if its an everyday thing and nothing for the dog to worry about, if he growls or barks at them, a stern NO, and reward with a treat when hes quiet is how i did it with the torts.
3. I'll get my puppy around the first of November. Would it be safe to take it visiting when I do the family holiday stuff? I'll have had it a month by that point, but I don't want to expose it to anything bad. I would like the chance to socialize it though. I do know I'll have to be extra careful if children are present.
If hes had all inoculations and has been toilet trained- i dont see why not. Just keep a good eye on him- or maybe take his crate/playpen ?
4. Are there any types of toys that would be dangerous to a puppy? I have an absolute TON of that end up laying around, so I'd most likely need to do a puppy-check on all of them. I'll need to puppy-proof my entire home, actually. O_O
There are some- generally dog toys will have a note on packaging if unsuitabe. Sorry I can't offer advice over the cat toys- i have no experience
5. Is it safe to let the puppy sleep in the bed with me? Should I avoid letting it until a certain age? I usually have two cats asleep there already...
If you dont mind it sleeping there for the rest of its life- it wouldnt harm the puppy, as long as its house broken already and you keep him at the foot of the bed- so you dont squash him in your sleep
6. Is there a certain brand of harness that anyone can recommend? I know that I'll need a harness for walking.
People seem to think Ebay is the best place- i never used a small harness for my last doggies as they where big enough for normal ones.
7. Same for food - any recommended brands? Right now I'm leaning towards Innova, since I feed Innova EVO to my cats and they're all incredibly healthy and have wonderful coats.
Id see what the breeder feeds them on, and make sure its something you can get in a local pet store. If you cant- you need to get a weeks worth from your breeder so you can gently fase it out over a week Mix his current food about 6 parts to 1 part new food, then the next day switch to 5 parts old food, 2 parts new food, day after that 4 parts old food, 3 parts new food, so on and so forth until you have fased out the old food completely. This change will need to be done gradually as to not upset your pups stomach.
8. Some friends have . Would it be dangerous to bring the yorkie to visit?
When he is big enough I dont see why not- as long as they are all well socialised and good with each other. Dont leave them alone though- and make sure its highly supervised.
9. Are there any questions I didn't ask, that I should be asking?
It depends what you already know Remember- ask as many questions as the only stupid one is one left un-asked. Good luck with your new furbaby and I hope he is happy and healthy when you get him 
