alright, my crate is just a simple milk crate with 5 pvc rod holders, but i was wondering what all you guys use and how i could upgrade my crate?

What do you want your crate to do?

basically hold a few rods, my net, and some tackle boxes

Customize it how you see fit. What's going to work for your style of fishing? What do you plan on carrying in the crate?

I used mine to hold a few tackle boxes, two rods and a net. I also used it to store my anchor during transit.

Since I've upgraded my kayak, I have no need for a crate, there's storage room everywhere for the rods, net, tackle boxes and net.

Google kayak crates and click on the images, maybe that will give you some ideas how to customize your crate. But in the end, you need to set it up for your style of fishing.

Good luck

I made my crate from an Itso Cube. I cut a lid for it from some polyethylene sheet, and hinged it with zip ties. I have a 3 rod rocket launcher type holder bolted to the back, and I made a holder for my pliers from a piece of PVC. I have a divider inside, and it holds 3 Plano 3700 boxes plus worm bags and several smaller tackle boxes. It's pretty big, and won't fit in a lot of kayaks, but it fits both of mine well. I made a couple of handles from paracord, and it works great!

I use an X-pak that has a strap and pockets you can place PVC pipe in to form extra rod holders.
I like it because it has pockets along the outside and a carry strap, and when I get the kayak out all I do is grab the strap on the crate and go.

Best investment you can make!
http://www.fishnyak.com/x-pak-crate-cover.html