Berkley makes a binder that you can keep the soft baits in. Is this what you are using? I think this is the best way to keep them. Its bulky but only when you have lots of plastics and any way you store them will be bulky. Thats the problem with lots of kinds of plastics but you can never have to many options. That is my story and I'm sticking to it. No one tell my wife otherwise...I think she almost believes me.
As for spooling with Fluoro here is what I find. I like the qualities of braid best: good line strength with small diameter, no stretch, and no memory. Personally, I hate memory in line and beacuse it has no stretch it is very sensitive. The stretch in both mono and fluoro also make it impossible to pop a dipsy. The problem is the visibility and with walleye fluoro will make a difference. So what I do is add at 10 to 15' of fluro as a leader usinig an albright knot ( I like the seagar's leader maker fluoro as it is very abrasive resitant - good for teeth). Here is a helpful site
http://www.animatedknots.com/indexfishing.php