It's beneficial to establish a standard folder and file-naming structure for your papers. It ensures that when collaborating with others, that your collaborators can find the information they need while working on the paper. In addition, it makes it much easier for the future you to access. The folder structure and file naming conventions that I use is below.

• Main Folder: Named (Conference or Journal Abbreviation) - (Short description of topic) - YYYY where YYYY is the four digit year of the conference
  • figures - the main folder that contains all the figures used in the paper
    • sources - a subfolder with the folder source files, if different than the included version. For example, this is where the raw plot files or the .svg files for figures will be kept.
    • unused - As the paper is edited, there are typically figures that are no longer included in the paper. I store them here, so that adding them back in later revisions is easy.
  • Submission documents - a folder containing any submission, registration, etc confirmations
  • Reviews - Most of my papers will be reviewed and require revision at least once before being accepted. I store those reviews here. I also find it helpful to store the initial submission versions of the paper here as well.

I name the .tex source file similarly to the folder, but avoid using spaces and replace the hyphen (-) with an underscore (_).

    ConfOrJourAbbrev_ShortDescriptionOfTopic_YYYY.tex

Some people might prefer to have the year at the beginning of the filename to make sorting via year easier. I prefer it this way because I am more likely to remember the conference or journal a piece of work appeared in more quickly than what year.

A screenshot demonstrating this folder structure for a paper I'm working on right now is shown below.