After being in the trade for quite a few years I got into a partnership with a couple other guy's including a guy that was strong on the business end. After being there for several years I sold my portion and have since started my own fire alarm company. I now sell to my old competition and do not market to the G.P.
There are many ways to track and manage all of the day to day paper work.
I use Excel and Word for everything except my books. This includes my own estimating program, P.O.'s, Change Orders, RFI's, Contracts, Proposals, Letterhead, Fax covers, Bids, and on and on. I think it is critical to put and get everything in writing. Peoples (Including mine) memories are questionable and a paper trail (including saving email.) has covered me too many times to count. Good Luck!
