Yeah in general build your spellset to have almost all your heals, DPS & combat buffs stuff. KA will sometimes try to swap a spell in, even during combat, but that's probably not what you want.
Then if you have a common reuse buff with a longer refresh and short duration, like Stance for knights, temp hp buffs from dru/sham you should dedicate a slot to them too. It will save you quite a bit of down time during buff phase. My SK keeps Stance, "disease" Skin and Harm/Concord Disruption. My Pal keeps Stance, Preservation & Harm/Concord Blessing perma-memmed.
Also, if it's a buff the puller may need often, I keep it on my perma-bar. The puller often runs out of camp so fast you don't have time to mem and refresh.
KA can use two slots to sub in spells as needed for buffs. One for regular buffs and one for stuff that will have a long memorization/refresh. I try to pick slots that have either non-combat stuff or low priority combat stuff. Like a DoT or fast-refresh self buff or such.
This would use slot 13 to swap in spells. It would load in 12 if the spell is going to take awhile to be ready. It would also replace the spell that was supposed to be in slots 12/13 after it was done. More on the Spells ini settings.
KA can also be setup to re-mem your spells at macro start [Spells] section settings:
LoadSpellSet=0 - just work with whatever you have memmed
LoadSpellSet=1 - load an EQ saved spellset from SpellSetName=
LoadSpellSet=2 - load the spells listed in your ini Spells section
While KA is running, "/writespells" will replace the spells in your ini with your current memmed spells.
Note: I think the older [MySpells] section is being retired and spell gems will now be in the [Spells] section.