I have the recovery file for my S4 mini and I have the new CyanogenMod ROM downloaded on my external SD along with my update file and gapps zip file but i'm not sure how to integrate the titanium update file into my ROM or do I just restart my phone and open that zip once the rom is installed?
You can normally install that zip through recovery itself once the ROM is done installing. So the steps would be:
Go into recovery.
Flash the titanium update.zip (just the way you flashed ROM and GApps).
Clear dalvic cache and cache.
Hope this helps.