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I would use transport for the transports and then in SEIV I always created my own class called "Fleet Support". This is where I dumped un-armed scouts, supply ships, and repair ships. In fact, once I get quantum reactors I create a repair ship with QR and send those out with the fleet, that way you save 20Kt of space on the combat ships for more combat capability.

As far as strategy I use "Ram Ship" because retreat in SEIV was not an option and you might as well try to hurt the enemy. I don't know yet how well retreat will work in SEV, certainly some ships get away.