"Saddles" for cheap... I rigged my trailer with cross members and to those cross members I added inexpensive plastic wheel chocks carefully positioned for proper support. I glued pieces of pool noodles to the wheel chocks for a little more cushion and carefully covered the chocks with black marine carpet to give it a finished look and added protection. Worked great. Each set of four "saddles" cost me less than $20.
As to rigging your boat. I'm fond of mounting rod holders on my crate. RAM's and Scotty's work well. I'm right handed and fish mostly off of my port side bow so I like to have my extra rods pointing toward my port side aft so as to reduce the chance of me snagging one on a back-cast. I end up drilling fewer holes in a boat because I rig my crate and that, IMO, helps resale value. Also, when I do buy a new boat (a bi-annual event it seems) I have less work to do to get it ready to fish since the crate moves easily from one boat to the next. Extensions are, IMO, a "must have" for the built in rod holders and I only put a rod in the one on my port side for the aforementioned reasons. I hate watching my reels take a dunking salt water.
Just my 2¢... worth every nickle you paid.