What is the best way or method to setup small business accounting so it makes sense?

What is the best way or method to setup small business accounting so it makes sense?
I have a small business that has been operating for a few years, but the accounting has been a nightmare partly because we never took the time to set it up right. We use Quickbooks Premiere to cut invoices, but that's just it, we dont use it to its full potential. My question is, what accounting methods are some of you small business owners (or cpa's) using? I am thinking of setting up a entirely new checking account just for monthly bills. Will this help with the confusion? I'm just tired of circulating money to buy more inventory and pay bills and not having the money go towards profits. If anyone can point me to the right direction or offer some advice, I would REALLY appreciate it. Hobby toy distribution to retailers and direct sales to consumers (online).