The term "command system" refers to the group of command buttons that appear in the lower left hand portion of your main H2OS screen.
H2OS is installed with a default command system that looks like this:

H2OS supports customizing this command system (that is, you can pick and choose which command buttons you want to appear, and their arrangement within the display, from commands stored in the H2OS commands library), and you can create one or more secondary command systems. If you have more then 1 command system available, you can choose which one will be active.
For all command systems, you can pick and choose which commands from the Commands Library are to appear in the command system, along with the arrangement of the commands in the displayed set (unlike the arrangement of tab pages in pagesets, which can also be customized, but which are always displayed in alphabetic order).
To access the Commands Library screen, navigate setup->commands or right click in the command system area of the main H2OS screen and select "customize command buttons")

The Commands Library screen will appear like this:

Because the primary command system is active, the Commands Library screen will contain command buttons for Details, Add, Delete, Browse and Pack

When working with a secondary command system, the actions you can take are limited to adding and removing commands from appearing in the command system when it's selected
This is because these commands are used to work with the underlying H2OS commands table, and (for internal programming reasons) this can be done only when the primary command system is in use.
By convention, all H2OS command systems are identified by the presence of the keyword "lmcmds" in the command system's file name.
The primary command system is named LMCMDS. It is stored in the PROFS folder
Secondary command systems are named LMCMDS_xxxxxx, where xxxxx is a name of your choosing. Examples include:
lmcmds_joes_accounting_commands
lmcmds_marys_management_commands
(note: don't use quotes or other special characters in these file names)
We suggest that you do not change the default command system (as installed), but instead create a clone of it (with your own name, see above) and customize the clone. You can designate your new command system to be the default using the setup->options->display screen.
See how to change command systems for instructions on how to switch command systems
This screen shot of the C:\H2OS\PROFS folder shows 2 command systems:
LMCMDS
LMCMDS_MYCMDSH

Each command system is comprised of 3 files (dbf/cdx/fpt), but is referred to by it's "root" name, so LMCMDS.DBF is referred to as LMCMDS, and as you can see in this display there are 3 files associated with LMCMDS (the DBF, a CDX and an FPT file).