If you are in the MY TEAM screen and you notice an Equip Best button here is what it does:

The Equip Best button takes the best gear that you have available for that soldier in your card collection and equips it to the space soldier you choose.

Please note that this function will even remove gear from soldiers that are not on your active roster and apply it to the soldier selected--this way you are guaranteed to have the best gear in your collection applied at all times.