I've prepared a document (which I've put on the website here, together with some scripts at this page) which I think is helpful, if you're trying to work out BCEA. I have never really thought of this, but I believe that when you write an academic software (or rather a library in this case) most of the times it grows out of a personal need. For example, I wrote BCEA while preparing a paper and as I went along I realised that it might be helpful in other circumstances too. But in doing so, you don't (or at least I didn't) realise immediately all the complications associated with making the software usable by other people. In this case what stroke me is that it's probably not enough to be a statistician to run BCEA.
Well, of course it helps a lot (and because the functions are not that complicated, it wouldn't take you long to figure it out!). But because the content-matter is quite specific you have to know what all the different functions actually are for before you can make sense of them. I realised this when I started thinking about a possible journal to which submit a paper discussing how BCEA works and what it does: on the one hand, a stats journal is probably not interested, because the stats behind it is not ground-breaking. But on the other hand a health economics journal may not be interested because computer programs are not their main business... So we'll have to figure something clever out!
Anyway, for the moment what I've done is to write a mini-manual describing one example in details. Specifically, I have some description of the actual model behind the economic evaluation (which to some extent one might even skip, if only really interested in learning how to use the package) and then a thorough discussion of how you work with BCEA (and kind of assuming that you've done the hard part $-$ ie developing the Bayesian model). However, I've put on the website also the files with the JAGS code and the R scripts to run it, so that, in theory, one can actually do the whole process (including the final economic analysis).