FTB and modded servers are really @tNt’s strenght.
But I think your problems are less of a FTB vareity, and more of a filesystem/storage.
Your USB-storage, is it formated for FAT32 ? or in one of the linux filesystems? USB storage usually come, and like to stay in FAT32. FAT32 have some limits in filename and file structure that linux file systems do not have. This means that you might have problems starting or running certain servers that need and use files that break with this filename policy. I had that problem a while ago when I used CIFS / SAMBA to attach a remote windows share to my MineOS installation: Setting up and starting a pocketmine server
As for dual boot:
I take it for granted that you know you cannot run both OS’es on a dualboot system at the same time? You can only run one or the other. So If you want to run your minecraft server on MineOS partition, but play minecraft with your windows partition this will not work. If this is what you wish to do, you need to look into virtualization instead of dual boot. Take a look at (For example) Virtuallbox: https://www.virtualbox.org/
I ask this, since MineOS really needs a virtual or physical host for it to be available whenever you want it, instead of when you wish to boot your windows machine into your MineOS partition.