Will I still be able to apply E-Business Suite patches and patch families, and add new modules?

Application Auditor has no impact on normal E-Business Suite operations, patches, or upgrades.

Patches and particularly upgrades may generate large numbers of database transactions that your AA would audit.  If you decide that patch and upgrade audit trails are not necessary, you may temporarily disable AA’s audits at the click of a mouse and re-enable them after any the patch or upgrade, or any non-standard DBA activity.

However, AA has identified undesirable activity performed by patch scripts.  You may find AA effective in preventing or highlighting patch issues.