I'm not having much trouble casting from the kayak. Things may be different depending on whether you have a SOT or an SIT. I have an Tarpon 120 (an SOT). I just let the line fall between my legs into the cockpit. That works ok. But another idea is to put a towel over your lap and let the fly line collect there.

I haven't tried the towel trick but I'm going to see how that works.