32u4 using internal clock on custom PCB - loading sketch
Yes you can reprogram your 32U4 chips via the ISP, they do not have to be fresh chip. If you set your Fuses to -U lfuse:w:0xE2:m -U hfuse:w:0xD8:m -U efuse:w:0xCB:m using AVRDUDE you will have an 8mhz internal RC oscillator set and you do not have to have the external crystal.

You can play with these settings at http://www.engbedded.com/fusecalc/.

I recommend learning the command line AVRDUDE commands this way you have more control over what you are doing to your chip.

I use this all the time, and if you need to do more than one quickly I typically make a batch file that does the Fuse Burn and hex at the same time.

this is for a attiny167 but you get the idea:
.\avrdude\avrdude -C".\avrdude\avrdude.conf" -v -pattiny167 -cstk500v2 -PCOM3 -Ulfuse:w:0xE2:m -Uhfuse:w:0xDF:m -Uefuse:w:0xFF:m  -Uflash:w:1060X01-001.hex:i