I’m not sure how you made your PCB (or if you had made one in the first place), but I made my first PCB (Xpandshield MK 1) without making schematics. I know where everything goes and where they go on the board, so I simply put the footprints and routed everything manually. Then I checked the PCB to make sure there is no violation.
On the more complicated Xpandshileld MK 2 I decide to again, not draw a schematic but the number of wires are troubling me quite a lot, so I created nets so I can assign each connection to a net. This way I can have the DRC checker (and the markings) working for me to make sure I don’t connect, say, the tri-state buffer in reverse polarity because I forgot which trace is positive.
Part of the reason I did not make a full schematic is because I use modules, like display modules and Arduino Micros that I do not have control over what gets put up there and, as a result, the symbols are lacking in the schematic designer (among others, but I can bear with it)
I’m not sure whether you are making a unit with no pre-assembled modules or whether you are making those with them. But since you had implemented the oscillator, my assumption is that you are not relying on external modules.
Anyhow. If you have a pin you are not using, you can put a “no connection” (usually a cross) flag on that pin. And have more nets. That is, if your PCB editor does not have a net editor (yet). They will make connections easier.
I usually use Eagle for personal projects and as a force of habit from my job and college days I always start by making the schematic. If I use modules I create a footprint for it and compile it into my own part library. I know it’s extra steps and not everyone needs to go through the rigmarole for simple projects but I’m used to the process so it’s not much of an inconvenience to me. Plus when you start getting into dense layouts, hundreds of components and 6+ layers making a schematic first pays dividends when you get to checking the finished design.
There is a free license for Eagle that’s limited but still good for most small designs. And if you are a student you can get the educational license for free which is basically unrestricted afaik. I actually never really got into kicad for more than messing around with it for an afternoon, but I’ve heard there have been a few notable improvements since I last tried so perhaps I should give it another chance.
You could try out EasyEDA. I was messing around with different pcb editors for my VFD project, I found EasyEDA to be (wait for it) the easiest! It’s pretty complete and has great tools for implementing specific parts with your board and it’s connected with JLCPCB. The only thing I don’t like about it is that it keeps projects in cloud storage. But that’s just me.