Custom SAMD21 PCB Crystal not working.

diabun is a little confusing. He meant to say two 6.8pF capacitors in series equals 3.4pF.

The standard crystal oscillator circuit used with microcontrollers involves two 22pF capacitors and a 1MHz - 24 MHz crystal.

Crystals are specified by the "load capacitance" typically 16pF e.g. two 22pF with 5pF stray capacitance.
If you have a crystal that needs a 9pF "load", e.g. two 12pF plus 3pF stray.

You are always going to have some stray capacitance. The smaller your physical components and careful layout can mean 2pF or so.

You can design things from first principles if you want.
Personally, I would take the "engineering" route. i.e. copy a proven pcb.
This means copy the part numbers for the crystals too.

David.