How do I write a check for an invoice to be paid and not use Schedule Payment?

invoices are what you use for your customer, your vendor invoices you his customer and that is your bill

So if you enter the bill, then use pay bills

other wise use an expense form, select the checking account as the payment source and fill in the blanks

Click the tiny arrow next to Schedule Payment

Click Mark as paid

Select what invoice or invoices you want to include in the vendor check. 

Or

Click the + New button

1. Then, select Check under the Vendor column. 
2. Next, from the Payee drop-down select the vendor you are writing the check for. 
3. After you select the vendor, all the outstanding Bills for the vendor will appear on the right side of the screen. At this point, you may choose the select all option, or add them each individually to the check. 
4. Now, just select save and close after you have verified the remaining fields on the check.