Yes, you can tow with your lowered truck, the real question is "How much can I tow and how will it ride?"
It depends on how much you lowered your truck. If you went with a mild two inch shackle drop in the back then it really should make very little difference from factory height. If you went with more than two inches then the biggest thing that you're going to run into is how the truck sits and are you hitting the bump stops. If you lowered it 4 inches you are going to be a lot closer to the bump stops so if you haven't already installed a shorter set of bump stops then now is the time to do it. If you lowered the back six inches with a flip kit you probably already had to cut the frame and install a c-section to get axle clearance. If you did this then you really can't make any more clearance.
But you can always install a set of air overload helpers so that you can add some air to the bags when you are towing to lift the back end up a bit and provide some clearance. We sell them at our air bag site https://airbagkits.ca