Merging two company databases

I have one company split between two databases, payroll on one, and the daily entries on the other. It's been this way for many years until our controller, who handled payroll & taxes had recently passed. Our accountant has adjusted one DB to reflect our last fiscal year end, which I will be running on solely once I've closed the current year. Since I'm transferring payroll to a separate database manually, I'm worried of the lack of history there will be and that I will need to go between DB's when doing ROE's or other reports. Does it matter if I enter year to date amounts or is manually re-entering all payroll detail best? I would love to hear from someone that has gone through a similar situation. Any tips would be very helpful.