Training Plan Question

In my forced recovery from Eagleman, I've been planning my training for the summer and early fall instead of actually working out. I plan on doing a century mid September and the Baltimore Marathon mid October.
I've been trying to make a hybrid of a century training program (10 week) and a marathon training program (16 week) to that end.
My question is this. If I alternate the long workout from each plan each week (ie. week 1 do long run, week 2 do long ride, week 3 long run, etc...) will I lose the training benefits from both plans and be a slow runner and a slow cyclist, or will the fitness I gain in one still be applicable to the other?
Thanks a bunch everybody.