The real problem is the lack of emulators supporting command line support for loading movies. I
What I'm using for editing movies is Maximus' TAS editor. http://tasvideos.org/forum/viewtopic.php?t=4448&highlight= For games that have random lag or a lot of randomness it will be hard/impossible to splice movies together. Also, the frame numbering in the TAS editor isn't equal to the emulator's frame numbering (I didn't check thoroughly, but frame 134 in VBA could be frame 133 in the TAS editor). So you should do something on the same frame (press A on the frame you want the two movies to be spliced together) and use that frame for reference. Of course, if you provide the two movies and the game name, maybe I or someone else can do it for you. But chances are you were running Super Metroid and I wouldn't think this game is hexedit-friendly...
Maybe you can find some information here. If you were intending to run Super Metroid, keep in mind that it's a very over-TASed game, it is being played on a very high quality level (saving every frame possible). And it has a lot of categories already. So probably it would be a good idea to run a lesser known game which doesn't have a published run. See here. However, it is said that you can learn from watching and investigating a published run. Also keep in mind that not every game qualifies for a good TAS. It's recommended you post on the forums about your TASing activities and in case you need help with something. TASing requires patience so you shouldn't aim to complete a 20 minute TAS in only 2 days. Try to put some effort into your movie and make it be interesting to watch. ...
If you are using FCEUX to record a NES movie, you can open and edit the movie files in notepad. This way you can splice movies together by cutting and pasting sections of input from one movie file to the other.
