Jay, the little seal goes on after the spring and retainer right before the two keepers. They don't really do much, suppose to keep some of the oil from running down the stems. Splash oil will still get the the stems for proper oiling, the seal is to keep pooling oil in the retainers from running down the stem. As long as they are on the stem, they should do what little they normally do. You shouldn't have any problems, I doubt they are much deeper then normal.
Joe