Many software programs lets people pay individually which is great, but bottom line the rent needs paid at the beginning of the month.

Some software will make adjustments for different number of bedrooms or bathrooms.

I'm 32, a software developer and my wife and I have 2 young children with a 3rd on the way. 

I know there are tons of software choices out there, but I don't see an option that would easily allow that.

In my case, if each of my two properties will be set up on their own LLCs and bank accounts, where do the funds come from for the subscription fee on the tenant management software that manages both properties?

I currently use Buildium, I find it's a good software for a Property Manager but not for an owner operator.

Do you utilize an accounting software already? 

There’s lots and lots of softwares that help you find who the owner is.If the owner is motivated and wants to sell, then you use a Purchase and sales agreement to get the property under contract. 

Do you have any specific software that you would recommend to any project managers just starting out or trying to transition to new technology?

Get one that can be tied into your Operations software, and not maintained on a side system.