@Skum1988 the majority of your issues are related to missing ROMs/folders. You don't need to create manually the folders for your ROMs - they are automatically created by RetroPie when the emulator for the system is installed. The fact that you manually created the folders means that:
the emulator for that system is missing
.. so the folder for the system is not configured in EmulationStation, so the ROMs don't show up.
I'd advise to make sure you have an emulator installed for the systems you want to play and - after you install it - restart EmulationStation. Each emulated system has its own documentation page in https://retropie.org.uk/docs/ which explains what emulators are available for the system, what extra files are needed (BIOS mainly) and what ROM/game extensions are supported.
For Dos games I also transferred the files from my pc folder and while I can see the MS DOS emulator I have no idea how to run my games (not even sure they are detected)
If the emulator is correctly installed, then the .exe /.com file used to start the game (or to install it) should appear in the PC system folder and can be used to launch it.
Last, but not least, when opening a support post, please try to include the information asked in https://retropie.org.uk/forum/topic/3/read-this-first to your post.
@korn16ftl3 transferring games via SSH/File shares is just as safe as the USB transfer and it's even easier/faster.