First thing is to make sure you have good syntax highlighting. This lists a few options: http://androidcracking.blogspot.com/search/label/syntax%20highlighting. I prefer Sublime syntax highlighting, because it helps check your syntax, and I wrote it.
If you have access to it, IDA Pro will show you control flow graphs, which can help you understand things at a high level. You can't do modifications from there and it's not free.
Rather than working entirely in Smali, consider using a decompiler. It will turn the Smali into something more high level. It will be easier to understand the code and pinpoint where you want to make changes. This will reduce the amount of Smali you'll need to ingest.
For decompilers, I recommend: