So only can do one job for all hours worked?  Or have to log each separately?

"I entered customer, service item, and payroll item in timesheets, but created paychecks without  checking the box that downloads it onto the paycheck, I manually added hours on paycheck. so now my job payroll cost do not show on my reports?"

You can Delete and recreate paychecks, as long as you are comfortable that you know how to control not sending anything already sent, confirm things are the same amount(s) as original, etc.

Or, in the Paycheck Details view, you need to assign Service item AND Job name to each line, which might mean you need to "reiterate" the Payroll item = add them again and again on the left side Payroll Item column, and reallocate the time, to end with the exact same taxes and takehome.

No matter what else happens, unless this is the current payroll run you have not yet sent, printed, etc, then you must keep a reference for how these looked Before you start making changes, so you can confirm it ended with the same tax and bank $ values, after your update.

"So only can do one job for all hours worked?  Or have to log each separately?"

You can break it down to any increment you want to.

Please see my attachments.