Above is a video on how seals / trails work, but the general idea is the following:
For those who are unable to watch the video due to whatever reason, the gist is you use /dm to go into the Seal Menu, buy a Seal or Trail, and then right click your Pixelmon to add the effect. There is a limit of 3 seals / trails per Pixelmon
Seals:
Fancy particle effects for Pixelmon when they first spawn outside of their pokeball
Trails:
Fancy particle effects for when you throw out your Pixelmon