In what direction? I have great experience standing stairs on end and geomerging them straight down, but haven't merged the bottom into the floor too often. I know why you want help though. The odd angles make them much harder to merge with geometry. All I usually do is brace the crap out of the whole thing, put some doors in the top, and hope for the best. One thing I've thought of but have never actually tried is to merge a double wall completely through the floor and using that as a guard to keep the stairs from entering the floor at a non-horizontal angle.
Go under the map and brace it there. Then brace all other sides except the one you are merging. Then use the save and quit method in matty's geomerging tuts in Forging 101. now carry on with your ordinary merge.