So: there are various alternatives to EAGLE - KiCAD, Diptrace - but it’s popular partly owing to its penetration and the volume of libraries available.
It’s worth noting that EAGLE is both a schematic tool and a PCB tool: you lay out parts in a schematic, and then, when all the ‘nets’ are correct on the schematic, it lets you make a board with those parts and nets. Some tools do one or the other (schematics and/or layouts).
Planning panel layout: I will sketch on pen and paper, maybe in graphics tools, but then I have to wrangle the parts into place and have to be constrained by how they’ll go together. Though I’m also more interested than some designers in ergonomics - I very much like Olivier Gillet’s attitude to “how big a finger is” rather than an obsession with fitting lots into 4HP.
So: sometimes parts don’t exist, and I have to make them - lots of staring at datasheets. But there are lots of good
lbr files out there, in particular, I use the Sparkfun/Adafruit ones, and also a pile of the EAGLE defaults. But making your own is an important part of the process - even if the pins and pads are right, the silkscreen might need updating to personal preferences. (I have my own parts for things like Eurorack power connectors, particular silks for opamps and resistors, particular switches I couldn’t find existing parts for.
Stacking boards is a bit of a faff: some people like multiple EAGLE files, some people put them in the same file. The key is ensuring that, relatively, headers are in the same place; beyond that, there are good open-source examples to copy.
In terms of 3D: I’ve been known to make sketches in Fusion360 of 3D parts, to imagine how they’d fit together - even just as solid boxes - but most of my synthesizer stuff has been pretty easy to imagine flat.
I use OSHpark’s own CAM processor files for making Gerbers, and also for DRU - design rule checking. This will make more sense when you’ve started down that road.
The other thing is: EAGLE is really non-intuitive, and I learned all this slowly - and using a lot of the open-source files that are out there.