In order to get a good answer there are a few things you'll need to post;
First of all how much water? (GPH)
Second what does the drain look like on top, and at the sump? (at the tank is there a place to introduce air? at the sump are your drains submerged?)
Also speaking more to the design issue than the drain problem ...why are you splitting it? If it's to feed a refugium you would do well to ball valve it so as to have control over flow to each.