I used to use TMPGEnc all the time. If you are doing MPEG2, then you go to the settings for the project, the advanced tab, then select deinterlace, and select the type. You can preview what each one looks like to decide what you want.
When I was encoding a lot of DivX I would use the deinterlacing built into the codec. To do that you would have to save your project as and AVI, the select the video codec, DivX, then you can hit settings. Go to General Paramaters, and you can select there to deinterlace.
Either way is pretty simple. You just have to wait to encode the video.
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-Michael
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