Hi Jordan,
Welcome to the club!
You’ve had a flying start and we’ll try to keep your speed up :-)
A few points:
1. Keyboard layouts, including those produced by Ukelele, (re)define only character keys, not "special" keys like Enter, fn, or the cursor keys.
So installing and activating a custom keyboard layout won’t affect how you use the fn key.
2. When you choose View > Keyboard Type in Ukelele, you get to choose a layout, e.g. "Powerbook USB internal".
But look to the right in that dialog box: there is a drop-down menu probably saying "ISO". Change that to "ANSI" and the onscreen layout in Ukelele will match your physical keyboard quite well.
It may not be matching 100%, but remember: this is just a rendering of the database of keys and their assignments that is inside the keyboard layout. In other words: Even if a physical key is shown in a different place here – or completely missing on the displayed keyboard! – you can still redefine it with Ukelele.
3. As Tom already wrote, the files coming with the App can be stored anywhere, but I wouldn’t put them in the place designated for installed custom layouts!
I have put them with Ukelele, like you wrote: "Should I put them in a sub folder of the Application folder together with the .app file?"
By the way, the text shown above the two folders "Resources" and "Documentation" actually reads "Copy these folders to your disk", giving you the choice. If you have a "Studio" folder with files related to creating custom keyboards, that could also be a good place.