Is one better than the other? Is there anything positive and/or negative in using both? Looking at the usage options it seems that setting any value for frameskip means that autoframeskip must be disabled anyway...so it seems like I should just use one or the other.
-fs is really only useful with -noafs. -afs will change the frameskip level (which is set by -fs) based on how fast MAME is running. If you use -fs 5 with -afs, then MAME will steadily lower the frameskip automatically if it is running at 100%, until it reaches fskip 0. -noafs will stop that automatic changing of frameskip level, and it will remain at fskip 5. Of course, you can still change frameskip level by pressing F8 or F9.