I’m a new user without hardware development experience. I want to build my own mechanical keyboard. I used this awesome tool to generate a base PCB design https://builder.mrkeebs.com/ but it doesn’t have the wires connected.
I attempted to do it, but as soon as I click my mouse, it disappears. I’m not sure if it is because the wire is too close to a whole or something? Or do I need to create another layer?
The two overlapping holes in some of the “2” pads can indeed be a problem. Holes can not be drilled properly halfway through another hole and drills break easily in such situations. This can be enough reason for a PCB manufacturer to simply reject your design.
Having multiple pads with the same number is quite common though in KiCad, but there is no consensus of how to handle them. The current implementation is that pads with the same number always have to be connected by copper tracks, while in keyboards switches and buttons it’s common to have “wire bridges” built into the switch itself, so a layout of a keyboard matrix can be made easily on a single layer PCB.
I really think, as @paulvdh comments, you need to use the Kicad workflow to make your board.
Start with a schematic, draw and assign footprints to your symbols and then use your downloaded tool as a guide to position your footprints on a PCB.
The reason I dont want to start from scratch is that I don’t know how to perfectly align the keyboard plate with the pcb. (i.e. how to perfectly align keyboard switch holes). for a keyboard precision matters.
The zones don’t recalculate every time you add a trace, remove a trace, or move a trace that intersects with the zone. You need to manually recalculate the zone with the b key. To avoid having to regenerate the zone all the time you can select the button in the left-hand tool bar to hide the zone fill while you work, letting you recalculate the zones only when you need to check connectivity (to make sure you haven’t cut off pads that want to be connected to the zone) yet still see what you are doing.
There are some really well written FAQ entries on this site that you can access with the FAQ link in the right of the header bar of this website. But, that category isn’t well organized. One of the items there is an index of FAQ entries organized by category. You may want to bookmark this item so you can refer to it while learning.
The footprints in your project either aren’t from that GitHub repo, or are old versions. The screenshot that you provided have pins 1&2 swapped from your board. Never mind. It looks like the screenshot on the repo that you copied has pins 1 & 2 swapped by looking at the footprint source code. (In the source code pin1 is made of 2 parts while pin2 is a single oval pad with an oval hole.)
Also, it looks like pin 2 on your board are overlapping drill holes which most (all?) board manufacturers won’t like. But the latest footprint from the repo pin2 is an actual oval hole that many board houses are OK with.
I forget if the tutorials in the FAQ area cover best practices for replacing/updating footprints en masse, but I do recall it being discussed here on the forums. If you can’t figure it out, find it in the FAQs, or find helo with the forum search, ask and someone can help walk you through it.