Limited experience talking here, hopefully others with more experience will over-ride where Im wrong.
1.How often and how much should I feed her?
There are ways of working how much should be fed and you can then break it in to smaller portions to feed through the day, eg breakfast lunch and dinner.
Im not 100% sure how to work this out though. You can feed this in Kongs or different ways so pup has to work to get the food and its a bit of brain work for them (as long as a 6 week old isn't struggling to feed itself of course).
2.What should I be feeding her?
Whatever the breeder was to begin with and then you can introduce your preferred food slowly enough to not cause an upset tummy.
3.Do I get her puppy milk?
I would think its not necessary
1.Is it a good idea to have her in a crate next to my bed upstairs?
I did this and loved it. Sleep time only when going in the crate at night but if they're initially unhappy you can drop a hand on top of the crate for comfort.
It was much easier to be woken by movement in the crate and do a quick toilet stop and I had zero whining from my pup doing this. It didn't take long for her to sleep through the night (might be longer for a 6 week old puppy though) and no grumbles when I moved her out of my room when she could hold on through the night. Pick a spot you'll take her through the night (or day), keep pup on lead so they can't wander and start playing and say your toilet word when they go. Lots of praise and happiness when they do. (Don't forget to give time for poo as well).
2.If so, where should she be spending her time throughout the day? In the backyard or upstairs in my bedroom?
If you don't want her to toilet inside you'd be best off creating a safe area for her outside (as long as she has protection from the weather of course). If you're home you could have a mixture of both, making sure she has alone time to learn how to be by herself. (Make sure you have plenty of things for her to do when you aren't there to keep her amused).
3.Should I instead build her a pen in my upstairs bathroom and take her down whenever she needs to do her business?
I think stick with crate beside bed. Its easier to wake when you hear them start to move around.
1.Should I be taking her out for walks? or is playing with her in the backyard enough exercise?
I think the rule if five minutes for month of age.
2.Also, when will I be able to take her out to the park for exercise? Is it after the second or third vaccination?
Id be waiting for final vaccination and however long Vet says for immunity to kick in before going to public areas (if she's going to be put on the ground). You can take her wherever you like in your arms for POSITIVE experiences. So be prepared to back away if she shows signs of being overwhelmed. Treats and praise for calm behaviour will help encourage that. Be careful of her meeting other dogs. Two things can go wrong - she has a bad experience which can be hard for a pup to recover from, or the opposite, other dogs become a huge focus for her and you're somewhere there in the background.
There's a lot more detail which could be added but you've asked a lot of big questions. Do you have any books? The Focussed Puppy is a great one to give idea on raising a well rounded puppy. Also 'Before you get your puppy' and 'After you get your puppy' are free downloads which are also full of good advice.
Good luck. :)