The SCons users guide is far from perfect, but it's reasonably good as software documentation goes: (users guide). The man page is actually quite a good reference, but in my opinion not such a good guide.
I have specific recommendations for parts of the users guide to read.
Finally, I put together a page on construction variables which talks about variables that control details of how targets are built. I think the users guide introduces these way late and doesn't motivate the problem at all.