Johnnybub - I would go with DriftMaster Rod Holders. They have numerous types of bases that can be atached to the gunwales. The rod holders also come in various styles so you can pick out the models that you prefer. I have 10 of the circular bases mounted on the deck of my Nitro 896. They are very low profile and have no issue with tripping on the carpet.
Bill, could you post a picture of your rod holders? I want to get a couple on my 896 for trolling in Canada. It gets old real quick holding a rod for 6 hours.
Johnny - I had the exact same boat, what I did was use the Driftmasters up front on the gunwales and in back I used a Roberts side mounted removable set (one on either side mounted just flush with the rear deck) to hole my off-shore rods for U-rig trolling for stripers.
The driftmasters worked great for regular crappie rods, but didn't hold my long poles for stripers.
Click on the web site below and you can see ALL the style of holders as well as the various bases that are offered. They are also in the BPS catalogs. I like the new models that allow you to have your rod at a 15 degree angle OR horizontal 'cause then you can use them for different types of fishing.