Hi Emily,
I just unscrewed the top cap off my fork - it's different to yours, it's a Rock Shox Tora (this years) and it has a schrader valve sticking out like a schrader tube would have. My pump connects to this. The pump I have is just a giant brand.
Since I don't have negative air (only positive air in one leg) I would say that your bottom valve is for negative air & the top for positive. I know the Rock Shox Reba Fork comes with positive & negative air so you could google on that for an idea of settings - if you can't find anything on yours.
Sorry I can't help with your other question but to me it does look like something is missing - or it's made for a different pump. If you get nowhere ask your LBS or Rock Shox themselves. It's a fair enough question.
I found this on the sram / rockshox site, you may find it useful down the track even if it doesn't answer your current problem (I haven't read it in detail myself).
http://www.sram.com/_media/techdocs/...rviceGuide.pdf



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