Can i state something in my rental agreement referring to the specific water and electric over usage? 

However, since you're renting by the room, it would still be tricky to bill folks based on their individual usage.

Basically it's a legal way to bill back utility usage based on # of bedrooms, occupants and the master meter bill.

We do not see how the homeowner is responsible for the usage of the tenant but we also do not want liens placed on our homes. 

You can stream line between tenants if these utilities stay in your name, and you can keep an eye on usage. many utilities require a deposit so tenants may be discouraged having so many deposits to pay up front.

Not all advices are inappropriate, take it as a grain of salt,move on if you don't like it.

She's section 8 so you can't raise the rent to compensate you for the changed usage of your property.

If that information is freely available then we might as well make efficient usage of it.

However, in "greening" the building it holds the tenants now accountable for responsible usage of utilities and waste and in the long run saves everyone money and provides them with a much higher quality place to live for the same $.

You can then deduct the expenses (% of usage) through your LLC.