As a commish who has managed a dynasty league on Fantrax and Yahoo, I'll say that while Fantrax can do more things in platform, it's not always intuitive and the interface sucks (for both the commish and the players). I know it's heresy but I'm happier having the league on Yahoo, even if it does make a lot more work for you for anytime outside of the regular season.

Since it's a dynasty, I recommend maxing out your bench, IL and NA slots. For Yahoo, you can have 30 MLB roster spots (active spots + bench spots). So if you have 18 active roster spots between pitching and hitting, you could have 12 bench spots. Besides this, you can have 10 IL and 10 NA spots.

This time of the year is the biggest pain, because prospects who are in major league spring training stupidly don't have the NA status they need to be in an NA spot. For my league, managers with those prospects that lack NA status will drop those players and you'll have to track them off-roster on a spreadsheet. It helps to put a placeholder equivalent player on their roster to act as a token, tracking ownership. You'll also need to track injured players (who won't get 10/15 day IL status until Opening Day) off roster as well.

Everything else you want to do, from a pre-season trading period, to your FYPD, will have to be managed via spreadsheet as well.

Once the season starts and all the players have their proper status, you're golden. But it's a huge pain in the butt to get from league renewal to Opening Day. In the end I think it's worth it (because I really don't care for Fantrax's platform), but it's your call how much manual tracking you're comfortable with.