I use an Excel spreadsheet. It only took an hour to make for all the months, business expenses, and financial year data (for revenue, reimbursements, and expenses). If you don't want to make one, go to the topic "New Mystery Shoppers" and you can download a free one that Flash made.
I have PayPal setup so that it notifies me when a payment has been made. A majority of each MSC's portal has a listing of shops you completed that make up a specific payment.
On my spreadsheet, I keep the job number and fill in whether or not that shop has been paid. Then I know what companies still owe me what. If I don't feel like going to the MSC's website because of time constraints, I can quickly match up what the company owes me to what they paid. If it's a match, then I just mark it as paid. A discrepancy of course means I have to double check the website.
It's time consuming either way, but it has to be done because you have to keep accurate records for tax purposes. Because you have around 300 shops to log for the fiscal year, now is the time to organize everything before it becomes too overwhelming.