There are two general rules for file organization: Be consistent and Be descriptive. You want to make sure you and your colleagues can find anything you and they are looking for quickly. You'll need to figure out which specifics make the most sense to you and document your convention in a place everyone in your research group can follow. Here are some guidelines to include in your convention:
How and when to save a new version is largely up to you and your research partners. Even if you're tracking changes with the software you're using, you should always keep a copy of the original unedited data available and save a new version when substantial changes are made
Most file naming conventions show new version by including a version number at the end of the file name, as in the example below, although there are other methods. Best practice is to be consistent.