Go to Navigator, select the project on which you want to apply the patch
Right click and select Team->Apply Patch
Select the patch file, click next
Select the project you want to apply patch to, click next
The patch created using GNU Diff has the root dir appended to in the start, select ignore leading path name segments as 1 to ignore the root dir and apply the patch correctly
Select the files shown in the list to be patched, click Finish