Find a co-op player and play through the game missions. I recommend assigning the squads with the host controlling the commander and Thaddeus/Thule and the support player taking Tarkus/Avitus/Cyrus. The ranged player handles suppression/grenades/explosives and the melee handles healing/support. This happened to work for us very well, however use whatever strategy works best for your playstyle.
It is best to communicate on your strategy on leveling and equipping your units in advance. Most people will want to concentrate on the mandatory missions, however keep an eye on the optional missions as an exceptional piece of gear can really make a difference in the endgame and boss battles. I like to equip the commander with a rally flag as it adds extra healing for your team, especially if you plan on melee tactics.
Keep an eye on your team at all times and look out for your buddy. Rez down commanders ASAP and retreat early to get those reenforcements back in the fight.
Stay together and communicate your plans ahead of time. You can alway type text in game by hitting [enter].
You can use the voice comms with live or in my case use ventrillo or one of the 3rd party comms setups.
It is best to keep your co-op game saved under a different file. On two occassions my partner played a few of the optional missions on our saved game and this did not affect our co-op playthrough. I have asked this quesion on the forum board for the game and the response from the developers is that both players must play the mandatory story missions.