All I do is wipe them clean with a tissue/cloth and store them. Then a quick lube before use. However, this may be overkill seeing that there are still many other o-rings in a housing that never get relief/maintenance until....
The only purpose for the silicone grease is to preserve the O-ring. It does nothing for the seal. On some sealed surfaces it makes it easier to slide the port body or port onto the sleeve or housing, but it does not add to the water-tightness of the seal. So the main point of adding silicone grease is to use it before storing, not after storing.
I clean the O-rings with a soft white face towel and maybe a little water. White lint is easier to spot if it sticks to a black O-ring. I clean all of the contact surfaces the same way. Then I look carefully for any lint, sand, dirt or hair that might remain. If lint from the cloth remains I may use a tissue. At my age - I wear reading glasses - I often use a magnifying glass to check the surfaces. It's a lot easier to see that tiny stuff that might stick to an O-ring and make a housing leak.
The O-rings in the push buttons can be lubed by using a Q-tip and silicone grease. I apply a bit of grease to the shaft with the button pushed out. Then I work the button until some of the grease reaches the O-ring. It leaves excess grease on the surface which can be wiped off. Ikelite will service every button in their housings by replacing the O-rings for about $100.