which option under "Find Updated Templates" will allow me to add the new code from 1.4.1 but still keep the modifications I made while i was running 1.2.x?
Diff - Performs a difference analysis between the templates and shows you exactly what changes have been made between your customised copy and the latest master copy.
i know what the diff page does. i have mybb 1.2.x right now and im wondering if i upgrade to 1.4.1 what will happen to all the custom edits i have on my templates. will i be able to keep my custom pages and templates while still allowing for the 1.4.1 changes?
Whatever is stored in the templates will be kept, and you will need to manually update the contents after you complete the upgrade.