The first statement is wrong. Don't know what you're doing but you apply transitions in secondaries the same way you do in the primary. No idea what the position tool has to do with it. You select the edit point in the secondary and double-click the transition you want or press Cmd-T for the default. The clips do have to be in line and adjacent to each other, but that's the same in any storyline or any NLE for that matter.
I think the other answers have pretty much nailed it - but just to confirm in point form:
- There is no such thing as a "secondary timeline" (the beginining of the confusion)
- What I believe you have is a bunch of clips "connected" to the main story line
- What you need, to create a transition between these attached clips, is a (secondary) "storyline" - by selecting the clips, Clip | Create Storyline