For toMOTko, it's easy because the glossary is already available here:

http://tomotko.sourceforge.net/en/glossaries.shtml

To use it, read the Getting started quickly section in the Help. You will find how to import an existing glossary. Be careful, you do not need to unzip the glossary file, import as is. The application wil unzip it for you.

The toMOTko application is not finished yet. I hope to complete it within a month. Nonetheless, even in its current state, it works well enough IMHO. You should have no problems to use it to learn Japanese.

If you have any other questions, don't hesitate to ask.