It's possible to change the CMOS time/date from DOS - I know tools that do it, but not any that let you do it from a batch file to a desired date/time. It's well possible that the built-in time and date commands of DOS can do this on systems with a RTC, but I don't recall.

As for changing CMOS settings, your BIOS maker would have had to have released a tool that does this for DOS, otherwise I'm afraid not. On Compaq systems there are tools for Win3x that can change many of the CMOS settings, for example.

Changing BIOS/CMOS data other than date/time from DOS is pretty much unheard of, and is certain to be system-specific.

What would those tools be?

Also what if the bios is a standard AMI or Award Bios?
this if for a VIA Epia Mini ITX Board.

What kind of changes are you talking about?

Changes to things like the Time and Date and Onboard device configuration such as Sound and MAC Address and Power on after power failure settings
and maybe any others that would be useful

I have booted into Pure DOS and have confirmed that the builtin DOS time and date commands do indeed set the Bios date and time

Your best option is probably to find ways to do what you want outside of the BIOS. Of course date/time can be set. If you are talking about a non plug and play OS like DOS you could just us alternate confg.sys and autoexec.bat files to load or not load drivers for the hardware that you wish to enable/disable, but that would not free up the IRQs that they use, if that is important. I don't think that there is anyway to change the MAC address without changing the hardware regardless.

As far as I remember, writing to port 70/71h could write data to the CMOS, but keep in mind some things:
- Different BIOS has different allocation for that data.
- I guess that changes has no effect until next reboot.
- You must update the data AND the checksum, or you'll get an error in the next reboot.

Ralf Brown's interrupt list documented some generic data, but things may be different in your PC.

Also, some NICs allow MAC changes via specific tools. Check your NIC vendor, maybe if has some tool of that kind.