Uh, the problem here is that we can't see what files you have to work with. Even then, why would you want to make a project like that if you don't know how to stitch the parts together?
I don't want to discourage you, but how about starting in a modular fashion?
My suggestion:
I would suggest starting off with a 3 1/2 " disk with your bootloader on it. Create a simple DOS first. Start by building a simple command prompt. Your boot loader calls the command prompt program. It's simple, yet you should start off slow. Then you have to design functions which other programs can call (via interrupt - just like DOS function 0x21) for file reading, writing, file seek, file open, etc.
Once your DOS is complete, then you can have your bootloader load the DOS module and then call your command.com program. You must also decide on how the data is going to be formatted on the disk. Perhaps the first 2 tracks can be dedicated to the disk directory.
You'll also need to design a sort of FAT table.
As you can see, creating your own DOS is quite challanging in itself.
After you have your DOS all ready, then try adding another module for additional features, such as memory allocation, or device drivers. The bootloader starts loading the different modules one after another, until it gets to the command.com program.
There is one problem though. If you use a DOS compiler or Assembler to create programs, the compiler and Assembler will create a DOS program. That is, the programs will have an .exe header. Your own DOS must be able to read it - unless you want to make time consuming modifications to the compiled .exe file. For experimenting around, I don't recommend creating your own style of .exe files. Read up on how the DOS .exe files are created, and the data structure of the .exe header.