1) md5sum your ISO like so:

md5sum ~/digimon.iso

And if it does not equal

512BA70738889081F262CBAFE5E49143
or
031400B3FEBB5C3B7CC5C83776C119F7

then you have an invalid ISO image and should obtain a new one. Save this hash for later (needed for choosing the correct patch)

2) Figure out if you want to use the sub or dub versions

3) Run

xdelta -d -f -s "/path/to/file" "/path/to/data/folder/HASH_sub_or_dub.xdelta" "/path/to/output/file"

HASH being the md5 hash of your ISO, and the sub/dub prefix. For example:

xdelta -d -f -s ~/digimon.iso ~/patch/data/031400B3FEBB5C3B7CC5C83776C119F7_dub.xdelta ~/digimon[patched].iso

I have not tested this, but there does not seem to be any black magic or advanced settings used within the GUI frontend so the previous should work. Also the update link is located at

http://digimonworldrd.wikispaces.com/file/view/updatefiles.csv

which provides direct links to the specific files, as well as their md5 hashes.