I would not hold out for a new version just yet, it appears there are quite a few issues that are being worked on and just because a version is "new" doesn't mean it's better, beta4 and the recent r121 are only recommended for experienced "testers" as things may go wrong and other things may not work at all.
Beta3 is still the current most stable release as you will discover by reading up a little, although I believe there are issues with the C1000, you will have to look in the forums for this as I don't have one.
As for package compatibility, most of the time packages will work on across versions but you can test it and see and if it doesn't work, remove it. Beta 3 has an awesome selection of precompiled packages to choose from so you wil be fine there.
And compiling your own is documented somewhere around here too.
One final note: Before you commit to running pdaxrom, be sure to realise that it is beta, and it may take more effort to get things working than sharp/cacko. But as most people here would tell you, it's worth it in the end
