Fising from a kayak, I fish muddy to stain, pads, weeds, rip rap and wood.  Mostly pads and hydrilla.  Setting up a box.

I have all my baits in idividual boxes by type:  worms by size, creatures, beaver, jig and pig, swimbait , spinner baits, frog, et c.  Lately, I take from those boxes to put in my two sided Plano boat box. But,  I have done it different ways:  1.  Take a couple boxes as they are, 2.  Take a little of everything.  3.  Take everything I can find in Junebug plastics with terminal gear (worked well, actually).  Looking for ideas when I can only take three rods and around 3 x 3700 boxes or a double side.  I either have too much crap and confuse myself, or too limited in my choices.  What would you do?

I’d buy this 

http://www.planomolding.com/v-crate

Thanks.  The problem that I have is that a milk crate won't fit in my yak.  Too narrow.  Plus my rotator cuff issues and back make it hard to reach back.

A yak to me is all about planning and fishing minimalist. Some guys drag 9 rods and more gear than I own bUT for me it's 3 rods or less and a bag with 4 3700 boxes.  If I plan to big bait it's a few baits and one rod.  Find your passion and roll with what works for you.  My terminal tackle is a smaller box that fits under my seat or in the side pocket of my bag.

K.I.S.S. One box for plastics and terminal equipment and the other for your frogs, topwater, lipless cranks, etc.  Don't concern yourself with color too much. With the soft plastics, you can bring along a jar or two of JJ's to change color if necessary.  With the hard baits, go dark or bright.  I find that too many choices have me switching out baits way too often and not working the water column with my confidence baits until I get bit.

Backpack, one 3700 box, one 3500 and a few bags of plastics...done.