The most simple way to use real floppy disks. Because the Enterprise using normal MS-DOS compatible disk format, any standard floppy disk is good.
You extract the downloaded program files to the floppy disks.
If you use EP32 emulator, then:
Use Hardware/Load memory config menu to load configuration. Select any which is contains EXDOS, for example 'original EP128 with EXDOS.cfg'
The EP32 automaticaly use your PC floppy drives as Enterprise drives. Important: before you start the EP32 then close all other windows which is accessing the floppy disk.
At the IS-BASIC prompt you can load programs with LOAD "filename.ext" command.
You can use many standard DOS commands, for example DIR, CD, etc
There is the EXDOS user manual.

The most of programs can be started by loading the .COM file.

is there a way to load from a folder in my hard drive (I mean,can I mount a folder in order to have the emulator treat it as floppy)?

For as floppy no.
But can you use for tape emulation.
You extract the program files to one folder in your hard drive. When you started the EP32 then load TAPE configuration file. And in the File menu use the 'select directory for tape files' and select your folder.
Now can you load files by the LOAD command.
If you not specify filename in the LOAD command, then pop-up window displayed and you can select what file want to load.