So I'm brand new to this and have the squad builder app, do the upgrades listed on the named pilot cards (Luke, Iden, et c.) get included with their main points or do those cards need to be all added in on the builder for the correct points total?

I'm guessing you're talking about Quick Build cards, and the listed upgrades there. Quickbuilds are a great way to familiarize yourself with the game, and play various different loadouts to a ship model, without having to think too hard about precisely balancing your list. It also allows for smaller-scale games, great for learning the rules without becoming overwhelmed by full squad strategy.

For Quickbuilds, everything listed on that card is included for one "threat" cost, typically ranging from one to five (though some extremely heavy ships go up to 6). Typically, a total threat level of 8 is considered to be a full standard game, so you can roughly equate 1 threat to 25 squad points in the squad builder (though, as @Lyianx pointed out below, the two systems aren't really cross-compatible). In the picture below, you would get Luke Skywalker, Instictive Aim, R2-D2, Proton Torpedoes, and S-Foils for 3 Threat.

That said, if you're fully customizing your ship, you need to take into account the full cost of each individual ship and upgrade. Looking at Luke, that means for the same loadout, you'd be paying separately for Luke (62), Instinctive Aim (1), Artoo (8), Proton Torps (13), and S-Foils (0), giving you a full ship cost of 84 points towards your full squad list of 200.

The quickbuild setups are not meant to be used in conjunction with the squad point system, but rather as an alternative to it.