First I would reiterate that modification of generated code has many problems associated with it and that, where possible it should be avoided. That said sometimes this is impractical to avoid or more effort than just dealing with the changes when the code is regenerated.
Sadly java doesn't support the concept of partial classes that c# has. These are precisely to solve this sort of problem.
You should see if your code generation tools support some form of meaningful comments which delimit regions added by yourself in the class (this is unlikely and won't help if you are modifying the code rather than adding to it)
You best option if you really wish to do this is to generate the files initially but check them into a version control repository immediately.
Then make your changes, check that in.
Next time you rerun the tools and let them overwrite the existing files you can diff against your source controlled ones and merge the changes back in (most trivial changes like addition of new columns/tables will be little effort.
This will not help you as much if the code generator suddenly generates radically different code (say a new version) but in those cases any code you added which wasn't simply additional convenience methods relying on data/methods already exposed publicly) will have problems no matter how it is mixed into the class. The version control system does still help however since it also records the original changes so you can see what you had added previously and what, one would assume, you need to recreate in the new style.