Fonts and Linux have always been quite the gong show in my experience.
The best way that I've found to keep track of things is to set up your X11/fonts directory with subdirs based upon manual viewing and matching of fonts. I have miscfixed, script, terminal, 75dpi, 100 dpi, oddball, and a few others. I have them in ttf, bdf, pcf, afm/pfa, fon. I'm sure I'm missing a couple types there. They are stored in my X11/fonts dir, ghostscript repository, /usr/share/fonts, individual app dirs, you name it, I've even found them in /etc.
About a year ago I was messing around, trying to clean them up so I knew exactly which fonts I had. So many of them are aliased. For example your LibreOffice might say you have Helvetica, but it's actually just an alias for Arial or something. Mix and match with known similar fonts is the order of the day.
So, in answer to your question, if you want to track and categorize your fonts, it's very much up to you which way you do it. XFontserver might help, but I found that program to be lacking robustness so bad I stopped using it years ago. xset can be your friend here too.
When I'm playing with fonts here's a script I use. It also has a bunch of commentary that may or may not make any sense.
Code:
#!/bin/sh
CMD="mkfontscale; mkfontdir"
DIR="$PWD"
for dir in $(find $DIR -type d | grep -v '\.'); do
echo "Entering $dir..."
cd $dir
echo $CMD
eval $CMD
# cd $DIR
done
#eval $CMD
fc-cache -fv
xset fp rehash
exit
# set your fontpaths
# xset fp+ fontdir
# xset fp rehash
# or edit XF86Config-4
#
# you can hand craft a 'fonts.alias' in the dir
# where a font lives. See miscfixed/fonts.alias
#
# gimp uses X fonts
# xpdf uses X fonts
# gsview uses ghostscript fonts
# OpenOffice uses X fonts but also supplies it's own
# God knows what Opera uses for fonts
#
# we have xlsfonts, fc-list
# there is stuff in /etc/fonts
# usr/(local/)share/fonts
# /usr/X11R6/lib/X11/fonts
#
#***
#
#If you add a directory, update fc-cache-1 AND
#/usr/X11R6/lib/X11/fs/config.
#
#If you add fonts to a directory, run
#
#mkfontscale; mkfontdir; fc-cache
#
#fc-cache -fv seems to rebuild X font collection.
#Font dirs are in /etc/fonts/fonts.conf and local.conf.
#
#in that dir. Once you're done fiddling with fonts.
#log in as root and do
#
#service xfs restart.
#
#Bob's yer uncle.
#
#Oh yeah, you can use /usr/share/fonts also.
#
#***
#
Take care and good luck.