AJ,
The Megaflow system has two parts. The front has slots and the innermost part is solid and acts as a dam for the box so yes, you can drain the box. After you drain it be sure to clean the area where the bulkhead gasket is going to seat. If the bulkhead is threaded, use silicone to coat the threads...much better than teflon tape and allows you to hand-tighten the fitting. If you need any more help, please feel free to ask.
Tom