OK. You're on the right track to start with. I believe we can pipe keyboard input into omxplayer from the command line and use that to control it. I'm just going to write it out, then explain what's happening
cat t | omxplayer --no-osd -b Media/test.flv &
echo p > t
First a special type of file called a FIFO, or first-in first-out file is created. Anything we write to the file comes out in the order it was put in when the file is read. The second command cats the output of this and pipes it into omxplayer. There's nothing in the file to start with though, so nothing happens. We wait 10 seconds. We then write "p" into the FIFO file with the echo command. Cat will then see this and pipe that to omxplayer, pausing the video. The last line just removes the FIFO file since we're done with it. If you're doing this lots though, you can just leave it there.