I do aikido as well as the SoP. My first note is that they seem to draw on a similar set of subtle muscles, and so doing one right before the other makes the later one feel harder: I find it works much better to space them by at least a few hours. In my case, aikido in the morning, SoP in the evening works wonderfully, but others may find different things work for them.

I'd personally recommend doing both to those interested: the relaxation exercises in aikido work wonders for the SoP and meditation; while the SoP makes perceiving and working with ki much easier.