For mods, the game reads all of the original files, then the contents of files the mods folder, replacing the specific things (data structures, constants, etc) in the original files with the values in the mod files. The mods override whatever was in the original source, and leave everything not mentioned unchanged.
For the focus trees, I expect the name of a "specific thing" in question is the focus_id field of a focus structure.
Code:
focus = {
id = USA_the_giant_wakes
icon = GFX_goal_generic_construct_civ_factory
prerequisite = { focus = USA_arsenal_of_democracy }
available = {
OR = {
has_war = yes
has_war_support > 0.3
}
democratic > 0.95
}
continue_if_invalid = yes
...
So, you should be able to put just one focus structure in your USA focus mod file with this ID, and whatever contents make the focus do what you want to do. You'll have to replace all of the values needed in that record (maybe just copy the original into your mod file to start), not just one line of the whole record. (Possibly you can overwrite individual fields of the record, but be prepared to copy the whole structure.)
If you want to insert entirely new focuses into the tree, I expect you're going to have to track down the other focus records for the items before and after and change their "prerequisite" fields to link the new focus into the tree where you want it.
(Caveat: I'm not a modder, so have no practical experience trying to rebuild parts of focus trees. The mods forum is probably the best place to get into the details of how to implement your mods.)