Depends. You can remove them, of course, but you might have problems if other programs need them. On the safe side, you can simply move them to another spot, then if something doesn't work, you can pop them back. As long as the spot isn't in your path (anywhere in your /home directory should do) you should be okay. You can use a similar technique for testing most files that you do edit.
For your startup, just add a link in /etc. You should have directories like /etc/rc.d, /etc/rc.0, or something similar. If you're booting into the GUI, then you need to edit rc.5 or whatever, and add a link to start your file. The best way is to look at the examples in those directories. 'cat <filename>' is the way to do it. Basically, it's just a file with the name of the file to run. There's also a number in front to tell you which files are getting run first, which is important if one needs to start before another.