If you're talking about the cooling system thermostat, I don't really think that it should impact air-conditioning cooling.
I assume that the air setting is on automatic & both the driver & passenger side controls are set at a temperature sufficiently low to cool the interior? If so, you need to have the system checked out.
If there is any chance that you are low on refrigerant, you want to disengage the a/c - shut it off - until you can have the situation taken care of, because running the unit while low on refigerant can take out the compressor & other expensive bits.