I separated my admin/management payroll into a separate company.  I plan to manually enter the p/r entries in GL-B as a total.  
 
Short of setting up another bank account, which I do not want to do, how do I get the checks recorded in the payroll check register of the regular company?

I would guess that the goal is to keep private the details of the paychecks? But, you need the net amounts in the check register for bank reconciliation?
 
You can enter the checks as a Type 3 Cash Disbursement under GL-B. Offset them to whatever account you are using for Net Pay in your summary transaction.

Thanks everyone.  We are trying to keep executive and admin payroll from general access by those processing the hourly payroll.  Being a small office and needing people cross trained, I did not want the person processing hourly pr to have access to all.  Same individuals do not have access to Change Companies.
 
ISTECH has an add-on program in GL-Q "Enter Payroll Checks".  It's a little pricey but it does answer the need of keeping the check register in balance.