First of all: you are using version control, right? Please tell me yes.
Eclipse isn't going to "change" your code at all. It'll put two or three files and dirs in the root of your project. That's it. Your code is the same as it was before.
If you move a class to another package in Eclipse (using drag&drop), it will automatically issue the necessary svn move command, and synch up the import statements everywhere. That's a 20 minute job done in 2 seconds.
Eclipse isn't going to "change" your code at all. It'll put two or three files and dirs in the root of your project. That's it. Your code is the same as it was before.