This. Make sure its rust free first. Install them, then caulk. I did the same, just the tops and sides. Left the bottom open, not to clean, but so any moisture that does get in can get out.
In reality, your more than likely going to have rust issues. Mine did not have any rust when installed. Couple years later I removed the rockers for upgrades and had rust. Nature of the beast.
F/S Dana 35, 4:10, open make an offer, local pick up only, will not ship. 3-8-13
My 1994 yj build page