I currently own 3 properties and I am quickly realizing that I don't have the proper systems in place to keep track of who owns what with regards to cash flow and revenues. I am looking for suggestions on how to best keep track of all of this. 

For Example:

House A - I own %50 and my partner owns %50

House B - 3 owners, split evenly

House C - I own %20 and my partner owns %20 and a 3rd owner has %60. 

We have an LLC for each property. An additional question is, does it make sense to have a separate bank account for each property or should they all flow into the same account? I am really just trying to simplify this as much as I can so that when we have 5,10,15 properties, it is easier to keep track of who owns what.

@Mitch Gilman

You'll read everwhere that each LLC should have its own bank account. It needs it to show that it is a separate operating entity. Furthermore, it sounds like you have, or should have, multi-member LLC's, so its taxed like a partnership and so in my layman's opinion, you should have a partnership agreement. Honestly, you should have a partnership agreement of some sort documenting how you are going to operate (how to split profits, who has decision authority or how its done, etc.). Taking care of these legal/accounting issues (seek advice from a professional) will automatically answer your question on how to keep track of your arrangements.

With the example provided, whether you have separate LLC's or separate standalone partnerships will need some detailed investigation/analysis. Some of it is a matter of your risk tolerance, some is just a legal/accounting issue.

I hope that helps.  Good luck.