I use this tool for sprite creation long time ago and i stop it because it wasn't... Hehe how do i say that... Look how can i import ALL Kae sprites in those 4 groups? Basic i only use them. As i see it i can only import 1 by 1 and there is over 500 of them...
As you see there is 4 group of parts, to switch between them you have to press ~ and use 1\2\3\4 keys for every group respectfully. But mine work flow goes around arranging needed parts in first group, and using rest three as storage for possibly usefull parts. So initially drag and drop all not used parts in first group to fourth group, just because they look bogus and we can use it only for getting some silhouette.
5) Look closely for sets of parts that you downloaded, and choose which one you like and will use in your ship. After this just drag and drop them to a groups 2-4. There is pretty much unlimited storage, but it can become really complicated to orient in them if there is too much parts, as it shows only in rows by 3, and to scroll it up and down you have to use only mouses scroll wheel.
6) Now drag and drop parts that you gonna use in your ship to first group. Close Group Arrange window by pressing Esc, and lets start constructing our ship.
So yeah, just drag and drop them in Group Arrange window, in any group you like. Select all of them in folder (ctrl+a, or just lasso em, or select first and shift click last) and just drag and drop in desired group. In group you can also select multiple parts by selecting one and then shift+click selecting whole bunch parts in between, and move after from group to group. To delete parts-select and press delete.
To open group arrange windo, go to Tools->group arrange
I recommend using first group as working group and the rest as storage. Every group can take 2-4 sets of parts without significant problem, and your working group will be filled with only usefull sprites.
Go to Tools->Save sprites ini. This will save our current sprite config. I recommend you to to use different sprite configs for different ships\ships series to not discontinue its "style".
To save you sprite groups profile, do what i said in quote. You can have specific sprite profile for every ship series, or ships individually, to not discontinue your style.