Great to see some more people multiboxing EQ2. I moved up to 3-boxing about 4 months ago after getting the whole innerspace/keyclone package sorted out but have been 2-boxing for a couple of years. With so many questions here, I'll just post some of my own findings in the hope that people find them useful too.

I prefer to have both slave instances use /assist for their targeting. This way heals will still land on the tank (or overzealous DPS) while nukes and the like will still land on the target. However, I also setup my healers 'special heal' (ward/reactive/HoT) to always go to the tank. Doing it this way allows me to have the tank switch to a different target (to spread the taunt love around) while the DPS & Healer continue to focus their fire on the first mob. This isn't normally needed though if you are by yourself. However, if you bring along friends/guildmates it helps to be able to maintain agro without having to rely on them assisting correctly.

Regarding an assist macro, that is quite simple. Just add an "/autoattack 1" after your "/assist <name>". The macro I use is a combination of "/assist <name>; /follow <name>; /acceptinvite; /accept_trade". As you can imagine, this macro gets a fair workout. Of note though is that my macro won't start combat until I start using combat arts or hit my auto attack button (I like having that extra control). I can't remember if there was an option to turn on autoattack automatically when assisting nor can I find an /accept_quest command

As mentioned, it is possible to add more than 2 spells to a macro but only 2 of them will fire off. More specifically, the first will start casting followed by the last one being queued. On the next press of the macro, the second spell will start casting while the second last spell will queue up. It will keep going like this until a spell's recast timer has finished. If you prefer to have a 'Blam!' button that casts each spell in sequence for each press, then just add a non-combat item (like mining) to the end of the macro. While it does add to the chat window spam, it does make the single key 'Blam!' button more useful. The same could be done with the 2 instant heals. Personally I use a couple of Blam! buttons. The first is just standard combat arts while the second one includes only those CAs that can interrupt or stun - great for using against casters.

Finally, something I haven't seen mentioned before for EQ2 is that sideways movement will not break /follow (as I believe it does for WoW). As such if you have the scout following the tank you can use your strafe keys to 'rubber band' your way around the tank and positioning yourself behind the target.

These thoughts and opinions are from a PVE perspective only.

Oh, and for those interested my active trios are:
Warlock/Berserker/Defiler
Swashbuckler/Shadowknight/Mystic
Mystic/Monk/Dirge