I am working on developing a new way to handle these slates which I think will be critical if the Fanduel Boost format stays in place. For now I have changed the way MVP's are handled for the standard single game slates on NBA and MLB. They are treated as a "faux" player, with an automatic 1.5x increase in their score. If you are uploading projections, you will only need to upload for the standard player and the 1.5x score will be automatically calculated. You can manually change the scores of the players and the MVP / non MVP version of the player should be updated accordingly.
If you play the single game format, please check it out and let me know if you have any feedback. I anticipate this being the way we handle the BOOST format as well if this works out.