Good morning, I am currently using Turbotenant for tenant screening/rent collection and reminders, and lease creation.

In addition to organized bookkeeping, Buildium provided other benefits that accounting only softwares do not, such as lease renewals with esignatures, maintenance requests, a tenant portal for rent collection, 1099 preparation for vendors. 

I even do my own taxes on turbo tax, but use management software to collect rent and track expenses.

Flip props, and collect the rent 

These are building improvements that likely won't impact your rent collection but you are still obligated to share in the costs.

When our tenants move in, we collect the first month’s rent along with a one-time, non-refundable move-in fee that’s typically a little less than half of the monthly rent (for example, $600 for a $1300 rental).

you should collecte deposit the moment the lease is signed or 24hours max. no deposit, the lease is void.

One of my criteria for investing is not to buy in any area where I would not feel comfortable sending my wife to collect rent in the dark.  

As for the security deposit, it will depend on the title that it was collected under, security deposit or advanced rent.

If you have more than one LLC, each LLC should have its own set of accounts.Checking: Collect all income here, then use it to pay bills, the mortgage, or maintenance.