You need to use the Insygnia Editor in PCS2. It's fairly intuitive and not difficult to use.
Then, set a graphic of your choice as a squadron logo of your ship in FRED.
You might also want a nameplate. Creating it is a bit more difficult, but not much. You'll need GIMP for that. Just make a 512x64 pixels file, fill it with alpha (select all and press delete), type your name as white text in GIMP (I forgot which font is used in Mediavps nameplates), center it and save it with .dds, BC3/DXT5 compression (don't forget that you need a DDS plugin for GIMP). Then use "Texture replacement" option in FRED to replace "nameplate" texture with your nameplate. Not all ships are supported, and making Orion nameplates is even more complicated, but for most capships in Mediavps, this should work.