honestly I wouldn't bother with including more voltages. the only one i could think of that would be useful to have on hand is 3.3V, to interface things like FPGAs, SD Cards, and a Raspberry Pi (and pico) if you're into that.
If you actually want to get into sound generation it should be somewhat straight forward to just use some existing chip like a YM3812 or SN76489, which don't require any negative voltages for their Amp circuitry, so i'm sure you'll be fine with just having 5V for now.
and one question i always had whenever i saw someone post about their retro computer but never bothered to ask... why an EEPROM over a FLASH chip?
i don't really see the appeal... unless you already had some lying around, or got an old programmer that cannot handle Flash (or don't want to spend time turning an Arduino into a Flash Programmer)
Flash is much faster, comes in higher capacities (not that relevant for an 8 bit CPU, but more for something like the 65C816 or 68k), and is usually much cheaper brand new.
also in your schematic at the Interrupt logic, why not have the output of the 74HC148 go to D1-D2 instead of D0-D2? that way you save yourself a shift instruction when handling Interrupts.
a bit more detail in the primer:
http://www.6502.org/mini-projects/prior ... coder.htmloverall it's a pretty neat looking board and i'll hope you make lots of cards for it!
though personally i would've used KiCad's "Conn_02x<number>_Odd_Even" symbol for the expansion connectors. as they look a lot closer to the actual footprint, so it's easer to wrap your head around where each pin is gonna end up on the PCB.