1) When interviewing possible contractors what questions should be asked? Is it possible to get an idea of their billing fees? I would like to weed out the good from the bad and have a couple teed up once I purchased.
I am a general contractor and in my experience billing is almost always one of the main questions and its in your right to ask it. Always ask if they have done full house flips many contractors "can do it" but take a much longer time then you'd like. Ask them what they do in house and what is subbed out. Examples of work if possible so you can see attention to detail.
2) Once a home is purchased and the remodel has begun how do you all know what colors to paint the walls, appliances to purchase, fixtures to purchase and general landscaping ideas. I am pretty creative but not in this way.
In all honesty it is completely up to you. Some people like to follow new construction trends. Some people like to be a little more bold. Best thing you can do is try to find out the trends in your market. talk to realtors and go to NREIA meetings.
3) For the Bay Area residents are there any discount retailers you go to to purchase appliances/fixtures other than Home Depot? I have heard there are some retailers that sell paint, tile and other material at a discount due to excess supply?
Sherwin williams almost always offers discounts through their local NREIA chapter as do many other local businesses.