I entered all my Buisness incomes and expenses for two rental properties. Now it is saying that I have to enter them on 2 separate schedule c's. I'm confused how to do this for two different properties. Do I have to delete all the work I already entered?

The two rentals could both be Sch E, or one Sch E and one Sch C or they would both be on one Sch C. They are either:

• Sch C rentals where you are providing services or 
• Rentals where you just collect rent every so often.

IRS Pub 527 states "If you provide substantial services that are primarily for your tenant's convenience, such as regular cleaning, changing linen, or maid service, report your rental income and expenses on Schedule C (Form 1040). Substantial services do not include the furnishing of heat and light, cleaning of public areas, trash collection, etc." 

Why are you saying you should have 2 Sch Cs?