When it comes to decoding your M/S recording using a Zoom H6 you only really have two options. Either setting the H6 handle it or decode your recording later in Post. The preferred method would be the latter, this is because you have more control over the amount of Mid & Side your recording will have allowing you to dial in the perfect amount.
Decoding your M/S recordings manually can be a bit of a faff and requires three steps. Split your audio into mono, duplicate the side recording and invert the phase on the duplicate. But wait, there's a much easier solution! Zoom have actually created a neat little bit of software that works as an insert called the ZOOM MS Mic Decoder which is free to download for both Mac & Windows.
YouTube tutorial demonstrating you how to use Zooms Mid-Side Mic Decoder.