It's funny, because I've seen people say different things about how you need to set the .conf file. However, I managed to get through the first installation error by setting both the EMS and XMS to false.
But, if you're installing from the disk-based version (the one available at Underdogs), you'll probably run into a second problem; the installation fails just as it completes, and it never writes the last file you need to run the game (sc.exe). This seems to happen to alot of people.
The first solution is to install Strike Commander through another emulator with Dos 6.22, then copy the directory over to where ever you've got Dosbox looking at.
The second solution is to use the Strike Commander CD instead. The ISO is floating around somewhere on the internet - P2P networks are the best place to start.
Of course, once you get it installed, there is a third problem people are having. On most computers, the game crashes and takes Dosbox with it just as you launch for a mission. This, I think, is a sound problem. If I don't setup my sound during installation, and just start the game, I can play without problems about 50% of the time.
However, once it crashes once, it seems it's done - something gets corrupted, and you have to install it over again.
If someone has an idea of how to fix that, I'm all ears.