Well done, Andrew. Congratulations, I'm sure your business will prosper.
As for Quickbooks, can't you create sub-items with different descriptions and prices? That's what I do - each of my clients has a negotiated rate - usually two tiered for on-site and off-site work (lower as an incentive for them to allow me to work at home).
Or is it a problem with the store software not working with this structure?