Dear Voiding.
You can customize your installation and upgrade in several ways. But those should be according to SAP recommendations. Should better to follow SAP documents regarding your issues.
Read following threads for EHP6 installation and upgrade for some odd cases
Also read this article.
https://websmp101.sap-ag.de/erp-ehp6-inst
Read following notes for further details
- 1064635 - SAP ERP Enhancement Packages: SP Stacks Release Info Note
- 1496212 - EHP6 for SAP ERP 6.0 SP stacks - Release & Information Note
- 1566412 - Enhancement package 6 for SAP ERP 6.0: Required SWC
[If you are having deficaulties for SAP note let me know to download for you..]
good luck.