If you want to do the T4's in Sage, you will need to create a 2nd employee for the RP0002 payroll, and do a negative 'paycheque' for the RP0001 employee and a positive paycheque for the RP0002 employee to move the RP0002 payroll over.  Unfortunately, Sage requires separate employee files any time a 2nd T4 slip is needed in a year, such as when an employee moves from RP0001 to RP0002 (i.e. every time a new employee is hired and goes onto your reduced-EI benefit plan after 3 months), or when an employee works in different provinces over the course of the year.

Thanks for your help!

Sage Support told me today that there isn't a way to do T4's in Sage 50 for two different payroll accounts. Can someone tell me how they are preparing/filing the T4s at the end of the year for both RP0001 and RP0002?

Sage Support is correct that there is no AUTOMATIC way to do T4's for multiple RP #'s.  However, you can pick and choose which employees to include when printing your T4's and T4 summary:  (Picture preview is fuzzy, but if you click on it, it should be readable).