Either ways is fine, but if you choose to upgrade the existing user, ensure that you an exported copy of the 9312 db, before upgrading with the sourceequalsdestination flag in the aut.properties to do in place upgrade

Refer this document for Upgrading from 9.3.1.2 to 9.3.3
http://docs.oracle.com/cd/E50306_04/otn/pdf/install/agaaz.pdf

Check your database version, becz if it is an lower version then you might need to upgrade the database. else run the AUT.

Note that the supported database version has changed. 11gR2.0.3 is the minimum version. Coming from 9.3.1 you are probably on 11gR2.0.1. Not a big deal unless you are in a validated environment and have to meet the vendor’s published requirements.

we are in 9.3.1.2. now we want to upgrade 9.3.3. can you please suggest with any DOC.
I have cleared all averify errors in agile db. and ran the latest AUT (p18696916_9_GENERIC.zip ).

can any one help from here. how to move further and what are the patches i need to download for db and applications side

To uprade database refer this document
http://docs.oracle.com/cd/E50306_04/otn/pdf/install/agaaz.pdf

and for hotfix merged into 9.3,3 refer this document
http://docs.oracle.com/cd/E50306_13/otn/pdf/install/html_agaaz/output/chapter_1.htm

Which OS you are installing, windows or Linux?

Am not installing new agile 9.3.3 , we are in agile 9.3.1.2 . so we want to upgrade to agile 9.3.3 from 9.3.1.2 . right now i have upgraded db with AUT. from here can you provide me what steps i need to do.

OS – Red Hat Linux -5

oracle DB – 11.2.0.3

In Agile PLM Upgrade means only Database Upgrade, and you can upgrade from 9.3.1.2 to 9.3.3 directly, by following the document sent by me earlier.

9.3.3 Application is fresh installation, so you have to uninstall the 9.3.1.2 application after upgrading db to 9.3.3. and then install the 9.3.3 application.

for 9.3.3 application Oracle recommends OS – Red Hat Linux -6.

Please follow the documentation the instruction is given very clearl