I'm going through a similar situation right now, although mine is refusing the 3rd nap (catnap) altogether. She's a little over 6 months now. It sounds like we're in the same boat, although our lo's are having difficulty with different naps.
During nap time, I usually just leave her if she wakes, but I keep an eye on whether she puts herself back to sleep or whether she stays up, because I can figure out when to put her down next. She usually puts herself back to sleep (well, most of the time). We've been slowly extending her A time, working our way toward 3 hours of A time so she's down to two naps. I think she's certainly ready for it, it has been helping little by little. If she wakes and can't get back to sleep, I try to help for 30-40 mins (sometimes I let her play quietly on her back for 10 mins, then try to get her back to sleep, that usually does the trick), then get her up, even though I know she's still tired. I keep her up though for her full A time if possible.
Hope this helps!
*HUGS*
Sonya =P