I'm not sure this is the best solution, but this is my setup: As the directory structure, I have a Podcasts subfolder, in which there are subfolders for each Podcast (audio or video). For example:
Podcasts The New Screen Savers show.png The New Screen Savers S01E01 First Episode Ever.mp4 [...] In Plex I have two Libraries set up, one for audio files based on the Music type, and one for video podcasts based on the TV Shows type. Both libraries use the same folder as their scanning location. Turn off the automatic matching by switching the agent to Personal Media Shows in the video library Advanced settings and Personal Media Artists for the audio library.
To keep audio files in order, use the track number field in the ID3 tags, especially when episode numbers are not in the file names.
For video podcasts you can set episode numbers by using the above naming structure (same as a normal TV show) to assign the episode number. Unless the podcast is split into "seasons" or other groupings, I would keep all items to Season 1. The Episode name is optional, but be careful that it doesn't start with E and a number, like The New Screen Savers Ep8 was titled "E3 with Jeff Gerstmann". The extra E3 in the file name was confusing the scraper as to which one was the actual episode number. In this case, leave the title off the file name, but add it to the file metadata and/or to Plex manually.
This doesn't pull in automatic metdata like poster art, but you can find art manually and add it to the same directory as show.ext if you want to.