If the money paid to your LLC goes directly into your personal accounts it is called comingling of funds and would be one factor in a future decision of whether the LLC is merely an alter ego of you personally.  

Also, since you mention in your email about "eventually" renting it out, he might be thinking that this is going to be a non-owner occupied property from the get go and may alter the terms of the any deal he could give you.  

Tenant shall not make any alterations or repairs without prior, written approval from Landlord.

They don't check every outlet, they can't remove or alter the property to look behind walls and more. 

Your agent might also have a suggestion on how you could possibly alter the deals structure to cover repairs.

They could cancel the policy, alter the policy, etc. since they control it.

In short, adding little bits of money at a time would (in retrospect) have a court consider the entity as an alter ego of yourself (and your partners) and subsequently "pierce the corporate veil". 

@Mahesh Dholariya - its possible that this area is designated open space which cannot be altered. 

Feel free to alter as needed.  

the IRS gets to alter real life to their version of reality :)