For the first steps the commandline is good enough. But if you plan using Sice for dos, it have to be booted to dos. In XP there is no way how to do this I think; in W98 you can press F8 at the very start - it will show you menu where you can chose to run dos. The other thing is that you can write yourself structured config - it will let you choose the whole configuration.
But I would really recomend you to use that VMWARE - (it must seem to you like advertisment
because if something goes wrong, then almost no harm is done, since you can backup those VMs. You can learn on it safely how to use fdisk, format, and other commands that you wouldn't try on your machine. Here you can practice safely...
Concerning running the files, just type in the filename and and press enter; beside that there are three types of executables - EXE,COM and BAT - exe and com are normal executables, bat are batch files. One more notice, there exists environment variable called path, it contains paths that are searched for executables. To be more clear - when you try to run executable, the system first looks into current directory, and then searches the path.
And the last thing - (I hope I remember it right) if files with the same name but different extensions, then bat is executed as default; if there is just com and exe then com is run.
Hope it helps,
least