At the very bottom of your dosbox.conf file is an [autoexec] header. Just input every command, one by one (each on a separate line) beneath that header and DOSBox will automatically enter them when it starts. For example, on mine it's configured as:
[autoexec]# Lines in this section will be run at startup.mount C C:\DOSBox-0.73\games\ -freesize 800C:
I don't automatically run anything since I have a whole bunch of DOS games set up on my computer, but that's what I use for mounting my directories and whatnot in advance. Assuming you don't know how to set up Daggerfall, I'll just point you in the direction of Bethesda's http://static.gamesas.com/downloads/games/daggerfall_legal_and_installation.pdf which should work perfectly fine for Daggerfall. Scanning over this, if I were to directly copy the directory names used in Bethesda's directions, you'd probably have something like this in your autoexec:
mount c c:\dosgames -freesize 1000mount d c:\dosgames\dfcd -t cdrom -label Daggerfallc:cd\daggerdagger