I don't understand what you mean by significantly affecting the system. I don't guess they're as significant as upgrading your kernel or your c libraries. j2sdk is a Software Development Kit or something? Java programming? And jre is the runtime environment. So you're a java programmer? I'd just install them like any other programs - configure, make, su, make install, exit, run - or whatever the details are for the packages. Well, except that I wouldn't because I'm not a programmer.