So you would want a separate dialog where you can select prepared spells and then have only those displayed? That is something I can make, but it is a lot of work and I am not sure about the implementation yet, so it might not be there in the next version yet.The mechanism I speak of is for memorizing/praying for spells at the end of each long rest. In other words, a way to choose spells after each long rest so that only those are shown on the sheet until the next long rest. So, at the end of a long rest, the whole spell list will reopen to choose again. I would also suggest adding a button that says, "Keep spells from last long rest?" That would allow the player to skip over choosing spells after a long rest if they plan on keeping the same spells from the last time they prayed/memorized spells.
As far as Fantasy Grounds is concerned, I posted the suggestion in their forum about importing the data from your exported format. I don't know if they will contact you or not about it. I also don't know if it is possible, or if it is possible, how much work it would take to make it possible (maybe too much). But, then again, it is only a suggestion.
The way I see it, it would be an option on every dialog for a caster that prepares spells to "only show prepared spells". Upon clicking "continue to next dialog" you would then be prompted to fill out all the spells you want to prepare.
I looked around for Fantasy Grounds and how they store their character data, but I came up empty-handed. I don't own an account or have ever played on Fantasy Grounds, so this is all new to me. Do you have a resource where they explain how their import/export looks like? It is a long shot, because even though it is probably possible to make a MPMB's sheet - to - Fantasy Grounds converter, that will be a whole separate piece of software that requires updates for every single tiny change in either my or their sheet. As you can understand, this wouldn't just be a small undertaking and can take a lot of time to develop, depending on how complex their system is (remember, I am only doing this in my spare time and it is limited).