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They all let you customize the height and width.
You really don't want large size FLV videos. The OLD and OUTDATED FLV codec that FFmpeg (and Super and all the freebie/shareware programs that use it) is good for maybe up to 640 x 480. Beyond that the size starts to negatively affect CPU usage. Remember that not everyone has a dual or quad core machine.
The first reply you got was the best reply. If encoding FLVs to 1024 x 768 select VP6-E codec; for any resolution higher use VP6-S codec. You can download Adobe Flash which comes with the encoder and use it for free for 30 days.
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