To get started you'll need an unmodifed Japanese version of SaGa 3. How you obtain that is up to you. Ideally it's from a ROM that you dumped yourself from an imported cartridge that you paid for. To ensure that the patch will work you can verify the CRC of the original and patched versions of the rom. CRC32 can be downloaded here:
Original Unmodified ROM: ADADA633 English Patch v0.2.612 597A986D
To patch the ROM, simply run the xdeltaUI.exe application included in the zip file. For the patch choose saga3eng_v0.2_r612.xdelta. For the source file select your umodified rom. The output file should be the name of the patched rom you wish to create. Finally click on the patch button. Once the patch has been applied you can run CRC32 on the patched rom ensure your CRC value matches the one above.