I basically do it like jlcnuke does.
A bit further: In my software (I use YNAB), I created a few extra categories, e.g.
1. Business Reimbursable - The outgoing expense is logged here. When it's repaid, it's income in the same category.
2. Business Portion - These are personal expenses that I get to claim a portion of on my taxes. So in the past my rent, phone, etc, went in here, and end of year I knew what to claim the percentage on.
If I'm reimbursed more than I spent, I just count it as income.
Sounds to me like essentially the same as what you do, OP, but the math is done for me (and there isn't a single cheque combing all of it).