In order to print multiple checks for one invoice in one day, you would need to created scheduled payments (those steps can be found here) for this invoice.  
You would create a scheduled payment for today's date, for example, and then one for tomorrow's date.  From the payments tab on the invoice, you will highlight the payment you want to pay, select "pay now" and you should be able to pay one separately.  

For example, if you have an invoice for $2500, and you need to create separate checks (for example, if two signatures are required for checks over the amount of $2500, and only one signer is in the office), you can create two scheduled payments (each for $1250) for different days, and print them on the same day.  This way the checks are under the amount that is required for two signatures.