While mod specific questions should probably be asked on the mod thread (Requiem's is here), the militia in Requiem are only slightly stronger than they are in the regular game and thus shouldn't be much of a problem. What version of the mod/game are you playing?
Also, Tarton's are the scout frigates, and will not attack unless you order them or you switch auto attack on, which maybe part of the problem. Some pro players like to use them to clear militia but for new players its better to stick with light and long range frigate early game (for the Empire in Requiem that is the Carrack Cruiser and Nebulon-B/2).
As for not being able to get all of the ships, most ship types require research before you deploy them. The infocard should show you the name of the tech you need to research to be able to build them.
