This is one of my main issues currently as well. There's no in-game way that I am aware of to identify a schematic as one that you already know. If you try to open the crew skills window to check, well, that won't work, since the game will only let you have two windows open at a time - and to get to your specific "manufacturing" crew skill detail panel, you first need to have the MAIN crew skill panel open. So, GTN + main crew skill window + specific crew skill window = 3 windows, which is obviously greater than the 2 window limit.
I could be missing something, and if so please let me know, but for now the only system I can think of to identify already known schematics while browsing the GTN is to keep a separate, out of game list going of all of my known schematics. Either that or have to close out of the GTN every time I see something I may not know, check my skill panel, reopen the GTN, reapply all my drop downs and filters and search again - which, really, no thanks.