I’d recommend keeping the signal digital for as long as possible, so you should go through S/PDIF if you are able to. Not only will this reduce the amount of noise/distortion introduce by extra analog components, it’ll also avoid any potential ADC the amp may be doing if it applies any DSP before outputting, which is extremely common in modern hardware.

Motherboard analog audio out is often noisy and generally not great. If you have an easy way to use SPDIF, coax or optical, you'd circumvent all that noise. If your amplifier has SPDIF reclocking, then even jitter would be eliminated. Even without that, chances are e SPDIF will be significantly better than analog out.

Only downside to SPDIF is that it's limited to 5.1 surround sound, so no 2nd subwoofer or top channel/ up firing speakers. If 5.1 is all you'll ever need you'll be fine with SPDIF