Watson, Gilman, et al's Recombinant DNA 2nd Edition was the ultimate source for me on all things DNA.
As for polymerases and protocols, Roche put out a trouble shooting flip-book (like 4in by 6in) guide 20-odd years ago that came in handy with difficult PCRs, but has since been replaced with everything being online these days.
If certain primers work on samples and some do not, that at least rules out sample related issues (i.e. contaminants in samples inhibiting PCR) and points to primer vagaries
There are a few simple rules you need to obey when designing primers but these are more guides than gospel to follow verbatim
Accordingly, find attached my SOP I devised to train students explaining such rules and freeware to use in detail
In addition, see body of this answer for prior answers I have put together on this subject