what you need to do is basically THIS:
You sim everything including draft, free agency, TCs, do "begin seasons" (that's when the schedule is worked out) and process all trades up until day 1 of the regular season. And now BEFORE you put in DCs for sim 1 SAVE the league file and copy it somewhere else (away from the FBB save folder).
My recommendation for preseason is this: Before you put in DCs, SAVE the league file under a different name (like "SSBApre1") but make sure to LOAD it again immediately (otherwise the folder where the HTML files are stored doesn't change). Now put in DC's, and before you sim save it again (if you are doing 2 preseason sims you can go back to this saved version and just input changes in DCs).
After the sim is run do NOT save it again - no need to store preseason results - just "output HTML" (remember, the data is now stored in "leaguedata\ssbapre1") and make the upload to the web site. Last season derek opened a special preseason website which i think is a great idea ("preseason.ssbabasketball.com")
If you plan on doing a 2nd preseason sim, it depends on how you do it. Either you sim days 1-20 for pre1 and 21-40 for pre2 or you sim days 1-20 for BOTH preseasons, that way poeple can easily compare results (btw, I use a minimum of 20-25 days for preseason because otherwise some teams would hardly have played 10 games).
If you decide to sim days 1-20/25 twice i would create subdirectories on that preseason web site (like "pre1" and "pre2") to have BOTH sims up for comparison. If you do the second one from day 21/26 there's no need for subdirectories, just upload the 2nd preseason sim over the first one.
AFTER preseason is finished, immediately copy the original league file back to the save folder and LOAD it, and don't forget to process all trades that have happened after you saved that file. That includes every move during and after preseason. I know some of those you have to process twice, once in preseason and now, but that's less work (and risk) than constantly switching between original and preseason league files.
Also, request that FULL DC's have to be posted for sim 1 since you are basically losing all the preseason DCs, so a "same" only means you have to zap through 2 preseason DC posts (in that case i use cpu rec
)
One more advice for simming in general: SAVE. Often and regularly. (Basically i have a save file in my league from after every sim for the whole season, just to be on the save side, but that's just me)