I have RSM130 and ER Nano skimmer. With both circulation pumps on I have microbubbles being blowen into main tank. So I wanted to move the skimmer across so it sits in front intake grate and the media rack to the other side near the heater sits. Has anyone done this or something similar?

That is going to be a tough spot since the media basket it designed for one area only. You may be able to turn it so that water will still flow through. So opposite the way it is to be installed normally. You will lose all water forcing and top rack features of the media basket, but it may fit.. probably won't thought.

Any small reef tank will have some microbubbles if you have a skimmer. If this is a new skimmer give it time to break in. If it is older well then a Tunze probably would have been a better choice.