There isn't a universal right answer.
\raggedbottom is of course an easier format to achieve as you lose the constraint on equalising page content.
If however you want \flushbottom then you have to ensure that the page content fits in the specified size. For example if your content consists entirely of lines of text on a 15 pt baseline with no stretchy white space between lines or paragraphs, and your text body height is not a multiple of that \baselineskip, then every page will be underfull as TeX cannot achieve the specified size so has to break a line short. The solution there is to adjust the \baselineskip and/or the \textheight to be compatible, or, if typesetting on a grid is not an absolute requirement, add some vertical stretch glue between lines (by giving \baselinestretch a plus component) or between paragraphs (by giving \parskip a plus component).
In the final editing stages using either you may want to adjust page size on a per-page (or per-spread) basis using \enlargethispage.
See also
Do I have to care about bad boxes?
setspacepackage or the\linespreadcommand? – egreg Jul 31 '12 at 14:57\usepackage[onehalfspacing]{setspace}\setstretch{1,15}. No I don't think I ever used\linespread. Difficult to produce a minimal example, since with \blindtext LaTeX will have no problems with either option, I suppose. And actually I do not really know from the log file to which pages of my text these badness messages refer (and it's a long document, the PDF having >250 pages). So it's not easy to reproduce the problems. Sorry. – lpdbw Jul 31 '12 at 15:25[1][2][3].... underfull box.... [4]...means the warning is about the stuff that appears on page 4. – David Carlisle Jul 31 '12 at 16:02