FRED is everything you need,place ships and make their beams fire either with mission specs(if you're using FRED2 Open)or beam-free-all for every ship(FRED2).
However keep in mind,if you have played the main campaign only,that FreeSpace and FRED have limits.Putting hundreds of warships is impossible,this "mania" or simply the curiosity a FS fan has to re-create enormous battles is called "Battle Of Endor Syndrome".
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I'm making a campaign with the Colossus as protegonist,I made four missions but now I'm concentrating on Steadfast and The Sagitta Project,I'll continue it later.