After those setpoints are entered, connect to the PLC, Go Online, and Save the PLC program. This will make the file you have saved match the entire contents of the logic and data in the PLC.
With RSLogix 500, when you download or upload and save, you get everything. Also, all data is retentive so nothing will automatically reset or change following a normal power cycle.
This keeps things fairly simple and straightforward, but if you will be frequently downloading files to the controller, it can in some cases be a headache.
If you can record the critical setpoint values in the PLC before you download, and then populate your offline file with the proper numbers, you can avoid the extra data entry. If you need to make small programming changes that don't include adding data table space or program files you can (usually) just perform online editing and then save it when you are done.