Is it okay to modify the LaTeX template for article submission with additional packages?
Unless explicitly forbidden, adding packages is usually ok and fully expected - e.g. in order to add support for listings, tables, symbols, encodings, operational utilities (extended macro/logic support), or specific features thereof. This should, however, never mean a general change in the appearance of the paper. Therefore, packages that globally alter fonts or font sizes are usually not allowed.

As for using a separate .bib file, you can usually work with that and (if explicitly requested by the guidelines - this varies a lot by publisher) copy the formatted information into the .tex file as late as for the camera-ready version (when nothing changes any more).