Welp, I was able to figure it out on my own. Because I'm a helpful guy, I'll go over my solution here so that people having the same problem might be able to find this thread in a Search.
Assuming you manage all your rips on another PC with a program like Ember or Media Companion and copy all the stuff over to an XBMC.
-Do all the scraping as you normally would. Edit the NFO files with your epbookmark tags. Use XMedia Recode and Calculator to determine the seconds value. Assuming you used Handbrake (or your DVD Ripper/Converter) correctly, your rips should have Chapter markers that make the start of episodes really easy to find. If the value of the episode is something like 45:26:046 (minutes
econds:milliseconds) use Calculator to determine the seconds value: 45x60 + 26.046 = 2726.046.
-Once that's all done, copy the show and episodes over to your XBMC machine. DO NOT copy the episode thumbnails generated by Ember or MC. And be sure to keep the original NFO files with your Bookmark values on your original PC. You'll need these as a backup.
-On your XBMC machine, Update your video library.
-Now when I did Shin Chan, it let me update the thumbnails by scraping Remote images. If it does, great, just do that. However, it wouldn't let me for Black Lagoon for some weird reason. If that's the case, go back to your TV show selection, bring up the info for the whole show, and press Refresh. YES for Refresh all episode infos and YES to Ignore and refresh from Internet.
-You'll probably get a new thumbnail for your show, but you should now have thumbnails for all your episodes.
-Because XBMC Overwrote your NFO files and their Bookmark values, just copy and overwrite the original NFO files (with your EPBookmark values) from your PC and optionally copy and overwrite your original TV Show/Season thumbnails, otherwise you can just scrape your original choices in XBMC.
-If the episodes don't play right, simply do another show refresh, EXCEPT make sure you Say YES for refreshing all episodes but NO when asking to Ignore and Refresh from internet. You'll have to refresh the show thumb (It's still there, just select local thumb and you should be set)
Now as I understand, show scraping works different from Skin to Skin. I'm using Metropolis, so YMMV.
Hope that helps people with the same problem.