So if you are bidding by square foot plus other variables this is what I would do.
Document your square footages for all different types of work. Ex carpet, tile, hardwood, flooring. Drywall, roofing, carpentry remodeling like moving walls removing walls etc. include different variables like moving furniture ladder heights etc. then track hours it takes to complete tasks. If your not making at least $60 per hour then do the math and prorate your square footage price so when the work is finished you are averaging $60 per hour. Or whatever the standard rate is for a contractor in your area.
Example. 100 square feet vinyl flooring takes you 5 hours and you charge $100. Your average rate is $20 per hour. Your charging $1 per square foot. Up your price to $3 per square foot and now you are making $60 per hour.