First of all, if you are running payroll in DBA then running it through Evo is the same.  
 
If you are currently using a different system and want to start running it in DBA/Evo then a quarter end (Such as July 1) would be a good time to start.  You need to create divisions (PR-M) and the PR-A to enter employees assigned to divisions.  To make sure the W-2 totals will be right at year end, run a "dummy payroll" for the total amount YTD or 2 (1 for each quarter) and manually edit all the taxes and other withholdings in PR-B  to make sure they match what was actually processed and reported on the 941 and state forms.

To check the tax tables, go to PR-F and do a lookup.  They should have a 12 in the far right.  If not, email me and I will send you the updated tables.  You also need to be on at least the January 2012 update to have the correct calculation logic in PR-B.