You're confused on what to do with all the frames after their captured? Try looking for a "Make movie" button. 
Disclaimer: The below advice is based on what I have heard about Helium Frog, and is not based on any personal experience.
I believe with HF to achieve pauses you will either need to capture that many frames, or do it in post-production. Onion skinning ain't that necessary, and when compared to having the raw frames backed up, as well as being able to directly manipulate them in the capture software, I think you should stick with MJ.
Now, should you switch, this is how you would create the necessary pauses in post.
With WMM, all you do is split the clip, and then import one of the original frames into the gap. That, or simply click the screenshot button. (I think that's how it works, but I haven't used it in a while.)
With Vegas, it's a bit more complicated. It doesn't have a handy-dandy split feature that I know of. And I'm not sure if it's just my copy, but the screen shot feature doesn't work. What I sometimes do is bring in another copy of the clip, cut each one to the same frame, then bring in that original frame, stick it in the middle and adjust its length as needed. The problem with this is it causes a noticeable bump when going from clip to frame. (Put this on full-screen, and then pay attention to the edges of the frame.)
I get around that by bringing in another clip and cutting it down to just the one frame, then stretching it out to the needed length. If it can't stretch that far, (Which commonly happens) I simply copy/paste.
Oh, and don't forget....
Spoiler (click to read)
You have now used all of your "Inquiry after information" wishes. If you wish to consult the Oracle of Awesomeness again, (AKA, Myself) try to figure the problem out on your own first. Then, if you can't find a solution, there is only one way that I will actually answer. First, you have to do the hokey-pokey, while reciting the ring-inscription (In Black-speech no less!) and eating an ice-cream sandwich all at the same time. And then you must bring me the Crimson Gumdrop, Jack Darter’s hat, Barry Hollows’ Oscar trophy, a pancake from Pancake Island, and three chocolate chip cookies. Then, and only then will I answer the question.
....Do all that, or if you just can't figure it out, just say please. But truthfully, most questions can be solved by simply searching the forums for a little while. Since chances are, someone before you has already posted about the issue.