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 you content consists entirely of lines of text on a 15pt 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 can not 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
plus component) or between paragraphs (by giving
In the final editing stages using either you may want to adjust page size on a per-page (or per-spread) basis using
Do I have to care about bad boxes?