I am not a Job Cost user, but I am a Work Order user and we had similar problems.  Originally, we would require workers to enter their time on the travelers that went around with work orders.  Then when the items were complete, we would enter that time by hand into Transaction Entry before completing the work order items into inventory.

I realize it seems to be archaic, but remember that Sage 100 is an ERP/accounting system... and while it has the ability to process data in very robust ways, it is very weak on the implementation of front ends for users.  *very* weak.  So for our operation, we have spent years of development creating the kinds of front ends that make getting data into our system much easier for people.  We wrote our own simple labor capture system (using Microsoft Access).  This system uses tables from MAS to allow users to scan barcodes on the work orders, and then scan the step they are working on, this writes a timestamp to a table.  When they are done, they scan the same barcodes, and it creates a stop transaction with a timestamp.  Now, before we complete the work order, we import the labor data for that work order from the Access database. 

There might be a third part tool like this available that integrates with MAS... not sure about that though. If you or any of your staff have the skills, you might consider creating something like I described.