I realise you want to encode the subtitles, which is why I explained how to encode the subtitles in my previous post.
You'll have to index if you want to modify scripts with the Script Creator or preview each script for adding it to the queue for encoding. The OneClick encoder is designed to make the whole process automatic.
My previous post described one way of doing indexing, step x step. If you open a source file with the File Indexer as I suggested, MeGUI will add the indexing job to the job queue, and from there you can run it by switching to the Queue tab.
I'll confess I didn't include instructions on how to open the File Indexer, because I assumed you knew all the Tools are found under the Tools menu, the File Indexer included.
If you open a source another way, via the File/Open menu for example, or by opening the Script Creator and selecting the source as the video input, MeGUI should offer to open the File Indexer for you, and from there the steps would be much the same as the steps I described in my previous post.