Coming from to trace and Kai CAD (which ended up driving me completely round the bend once they started changing library management every other new version) I did find it a bit strange. As I said the workflow is significantly different to other programs. I have become partial to Farnell's own brand of resistors and ceramic capacitors as I figure they are no worse than anyone else's and it will get me less questions from a subcontractor when they can't get stock of a specific manufacturer of 0805 resistor when in reality as long as it is 1% and the same PPM I don't really care who made it. Personally I use Farnell although I always avoid using distributor order codes as these can change at random and get assigned to a completely different part which is not helpful to a subcontractor who suddenly orders an expensive contactor instead of a resistor.
They seem to have a love for Digi Key which might help people in America as a lot of parts are already in there with Digi Key codes.
This is easily done as you can point software at any folder you like which contains libraries so you can initially run your own libraries in parallel until you decide you want to stop using theirs. I have now got to the point where I have completely eliminated their libraries and retained only the essential files required which define things like pads and holes that are subcomponents of footprints and symbols.
Personally I found it easier to start from scratch with my own symbols and footprints. The idea of generating components and footprints and managing the library from within the main schematic or PCB sections was quite the novelty but at the end of the day you get used to it and it saves you opening another window it's just a little bit hair raising at first to think that you are messing about with breaking down and putting symbols back together in the middle of your main design but at the end of the day it's okay and to a degree it means that you can be part way through drawing a symbol or a footprint and then just save your project and close it and know that the library part you are halfway through can be completed when you open it again. I bought the second-tier licence as I definitely wanted 3D CAD output and custom copper pours.
I too found this frustrating at first but if you persevere you will learn how to use it. I sort of get the gist of your frustration and what does need bearing in mind is that for some reason Proteus works in a completely different way to most other packages. Gerbers are simple to create with their CAM processor, if you post your project I am sure someone could if you needed it, create Gerbers for you. IMO it is a mid level package, comparable for me to something like CadStar, and if I were going to recommend a PCB "food chain" it would go something like: KiCAD -> DipTrace / Eagle -> Proteus -> Altium or OrCAD KiCAD being free, but very very usable, DT/Eagle being low to mid range, i'm sure you can read the discussions on these on the forums, if you have a spare year to sift through all of the divided opinions! Proteus is one of the best for simulation (of PIC's) and has a decent layout and capture tool, the only thing missing is as I say, high speed design, diff pairs, length matching etc, and Altium and OrCAD are on their own level. It has the usual 3D view, Gerber viewer, older graphics chips used to cause issues with drawing, not sure that is an issue these days. Their support, though i've never had to use it, seems to be very good, they seem to have a dedicated team of support engineers and they answer quite quickly through their forums, they have a YouTube channel with various videos. Overall a good package for the price (£4k for the "platinum" I think), the autorouter - meh, if you set it up correctly it will do a decent enough job, if you even use the AR, most don't, many will tell you it's a sin, I am an occasional sinner and it has produced workable results every time, then, most other packages have also. I used it in industry on V7, I have used V8 for testing purposes, and it is not much different. The layout tool "Ares" is missing some features for high speed design, but it is fully functional and is very easy to use. Depends on the package you opt for, but, Proteus is used in UK universities, it has some nice simulation features, the schematic capture is fully capable, and is very intuitive, creating parts etc is quite simple.