If you don't yet have a "business" bank account for this, open one. It will help you keep the flip expenses separate from your personal stuff. Make sure the debit card for the new account looks different than your personal one - that way you are less likely to swipe the wrong one at the store. If the bank offers free or really cheap personalization of the card, put a picture of a house on your business debit card. :) Ask other area investors which banks are good to work with.
If you think you might buy most of that $6,000 in materials from one store, you might ask around at the stores in your area (Home Depot, Lowe's, possibly Menards) to see if they have some kind of volume discount or contractor program. Sometimes you can get a flat percentage off or as a rebate; sometimes they'll send your order to their commercial desk and bid a slightly lower price.
Like @Brian Pulaski said, start up some file folders and spreadsheets. GET A RECEIPT FOR EVERYTHING and save it!
You might look into what the expense categories are for when you file your taxes. When I started rehabbing my rental, I kept all the physical receipts, and put them in a spreadsheet, but I didn't categorize them. At my first tax time, I had to go back through all of them and put them in the right categories. Now, I put the receipt in the correct category within a few days of when I get it, so I'm ready to go at tax time.
If you know you will need some new tools or equipment to finish the work, keep your eyes peeled for sales, especially here on Labor Day weekend. It's easy to go crazy with tools, but simple stuff like a new set of drill bits or screwdriver bits can make things go better during the rehab. You didn't mention appliances, but that's another thing to look for sales on.