Using a Runeword or Glyphword uses all 3 slots, so no you won't be able to put stones in them. Since several of them are more powerful than what you could get by adding 3 stones, it's worth it.
For the weapon, personally I do find Severance to be far and away the most brutal (see my comment below from January :) ). Geralt + full School of the Cat armor + Aerondight sword with Severance + Cat School Techniques general Skill + Whirl = Oh look there's a massive squad of enemies *blink eyes* Oh, nope, now there's just a large spread of body parts all over the ground. You quite literally don't have to worry anymore about being vastly outnumbered and surrounded.
For the Armor, the weight-change thing wasn't enough to warrant me doing a cross-build to make them effectively Light for the Cat School Techniques boost, since the natural buffs of the light armor also naturally tie into the build of a Light armor fast sword-swinger (particularly the better Stamina regeneration). I found I preferred the Protection enchantment for the immediate free Quen shield. But that's just me; I'm sure Sign-slinger builds based on Medium armor could find several of the Sign-based enchantments useful.