They multiply all at their same paces, although sometimes they multiply like nuts! To get rid all but one of them, right click them and then click "Reduce to One". This will reduce the selected shimeji you got (like Karkat, Eridan, etc.) to only one of them. It won't effect the others, however.
Yep! It should all work for all of mine and all of everybody else's. It's all basically one program, and everybody programs it in the same way.
How to get the program: [link] <--There's the link to just download, it, straight off of google. It's pretty simple after that, go into your downloads and you can open it up. First, however, you're going to need to get the image sets.
How to get the shimejis: So, I put mine in ZIP format for easy use. To get some in the format of .RAR files you'll need WinRAR, and that I can't exactly help you with. Download the ZIP file from me, and then open it up, copy the folder inside that should say something like "Karkat Vantas Shimeji by daniladawg" (or something like that), copy that folder. Then, open up the zip file that the program came in, until you find a folder called 'img'. Open up this folder and then paste the folder containing my material into the 'img' folder. You'll have to do this with each shimeji you want.
To start the program, back out of the 'img' folder, and then there should be a program icon called "shimeji-ee". This is the program, click on that and then select the shimejis you want to put on your screen. You should be done after that!
I'm sorry if this is confusing, if you'd like I might do a livestream next weekend showing the process.