You can pay your expenses any way you want. Cash, check, etc.... Enter these items into Quickbooks as needed. Keep the receipts in a file cabinet and set up a folder for each month. Once they are in the folder you will probably never look at them again. All the info is in QBs where you can get reports. For example, click on "fuel expense" and create a report for your monthly or yearly cost for fuel.
Having an accountant set up your QBs is a good idea. Get it set up right from the beginning will save a lot of grief later.