Payroll Import

I've been frustrated by this problem for a month since taking my new job.  Problem we're having is that it's taking payroll entirely too much time to enter each check manually, so I built a custom import for them to use and import as a .csv.  We pay by piece work that is averaged out by that department's daily output (people switch departments) so while they always have the same home department code, we don't have the same pay code for that person each day.  Every way I try to import or build something to import,  

I tried a few partner software, but none of those allow us to import our file which brings us back to the main problem- Payroll takes up too much time.  

If you've encountered this problem, perhaps you could share what you found worked? I found a Sage Peachtree reference in Visual Studio and I can most certianally build something, but I'd rather find a good system I can buy out of the box and focus on resolving other issues.

I feel like this is being made much harder than it really should be.

Thanks in advance!