You can use filename substitution;
I'd also recommend using better options for ffmpeg instead of sameq. It will use a larger bandwidth than necessary because it is trying to avoid any loss in quality using a lossy compression scheme.
Determine the optimum format and options for your needs or device and stick with it. The input doesn't matter much.
At work, I will convert commercials using ffmpeg.
This is the command I use for fixed 7MB/sec interlaced commercial spots:
ffmpeg -i <videoin> -f dvd -vcodec mpeg2video -pix_fmt yuv420p -vb 7000k -r 29.97 -minrate 7000k -maxrate 7000k -bufsize 800k -flags +ilme+ildct \
-acodec mp2 -ab 224000 -ar 44100 -pass 1 -vol 256 -y <vidout>.mpg
This is probably too high of bandwidth for longer videos. Most of the options are learned by trial and error when something new crops up, and is left in. you may also want to include the size and aspect ration of the output video.
For variable rate videos, look at the qmin and qmax values instead of minrate and maxrate.