Using dedicated bank accounts goes a long way towards making this easier. It sounds like you were mixing personal into the business cards. Not only is this frowned upon (and could cause liability issues depending on the entity type), but it makes things very complicated at year-end, as you're finding out. It's also tough to explain to the IRS if you get audited.
So:
Step 1 - get dedicated business accounts.
Step 2 - get something like Wave (free) or Xero (paid). Connect those bank accounts, and keep track during the year.
Step 3 - ???
Step 4 - Profit (also, not sure if you're old enough to get this joke if you're in college now).