I don't want to comingle funds by depositing this into my LLC bank account and I know I can't just modify the check so what should I do with these checks.

Completely free to set up all you have to do is pay a deposit for the appraisal and they reimburse you at closing.

I'd prefer to sign a new lease, but how do I managed the damages deposit?

There is much more to it than just buying a property, renting it out as and STR, and having money deposited in your bank. 

He's been calling the office harrassing my staff about getting his security deposit back. 

Not only is there a deposit, more importantly there is a air of accountability since the home will be checked IMMEDIATELY after a stay.For those of you with long term tenants, when is the last time you looked inside your home?   

Think of all the things that could go wrong and see if the lease addresses them: unauthorized pets or tenants, early termination, security deposit, lease violations, late rent, eviction, lawn maintenance, parking, etc.5.

@Jacob Chapman you have experience with Yardi so you should know what is important to track: rent charges and payments, security deposits, maintenance requests, tenant/vendor contacts, invoices, etc.There's a whole list of free software solutions available for small Landlords.

Or keep track and deduct from deposit

I was even thinking to do a bike rental where I can put the bikes in a storage room/garage with a smart lock, so when the guests paypal me the bike rent and deposit, I can send them the code to unlock the storage room/garage.