This is a very common situation for accountants with clients who own multiple enterprises. By some other answers, it's obvious one point should be clarified: although this is can be a huge bookkeeping headache; if he is the principal owner of all the businesses then this is in not a criminal activity if he has directed you to keep track. The is also true for personal expenses if he has directed you to record them as personal and not business.
Ideally, you will keep separate Quickbooks companies for each legal entity. This means the credit card activity for different companies is funneled through Balance Sheet Intercompany accounts. When the X company's credit card account is charged with an expense for Y company, it is coded to an Asset account "Interco-Due from Y". Correspondingly, in Quickbooks Y company, an entry is posted to the liability account "Interco-Due To X" and expensed accordingly. Personal expenses are treated as Owner Withdrawals from X Company.
Periodically (monthly is advised), a check is cut from Y Company to settle the Intercompany account.
The Intercompany accounts can also be settled by offsetting Owner Equity transactions but this method is not something I would advise as it easily confuses and clouds direct owner distributions.
Keeping all three companies' books in a single Quickbooks company would allow you to use Classes and so distribute the credit card activity that way. However, this is not advisable because of the difficulty in properly tracking and accounting for each companies' Balance Sheet accounts - particularly Owner's Equity. Not impossible, but requiring significant thoroughness and clarity of entries.
You should advise your boss that using a single credit card for all companies compounds your time entering credit card activity by a factor of 4 (duplicating each interco transaction x 2 companies) in addition you now have 4 additional accounts to reconcile each month. If you calculate your time spent and your wage/salary and give him the dollar amount the single card method costs him, he may relent and apply for 2 more cards.
If the companies have separate checking accounts, almost all major banks now offer free check card service. This would be a simple and quick way to get the transactions entered...especially if you use Online Banking!
Good luck!
Karl Sexton
Accounting On-Callâ„¢ Tampa
Accounting | Quickbooks | Tax | Bookkeeping
(813) 641-4262
www.accountingoncall.com