I will be building a deck this month and my question is about climatizing the cedar deck boards. They are 2X6 boards, and I will be putting a sealer/protectant on them after the deck is built. Should I wait a couple for months and let the cedar oils dissipate, or can I put the sealer on right away? Only the top planed surface will be sealed, the sides and bottom are being left rough.
You should have them dry out as much as possible. 2x6 boards take longer that the 5/4 boards, naturally. You don't want them to dry out too fast though - drying them in the sun is NOT the way to do it. The way I recommend is to stack them all in your garage or basement with spacers in between each board (1/2"-1" will do) and run an oscillating fan directed at them to help circulate the air and dry them out. 3-4 weeks should do it, slightly less if you have the room in your basement.
Make sure you sand the boards before you apply your stain - stain is much better than sealers as it lets the wood breathe. Sanding makes the wood accept the stain better. I recommend BM or Para stains to all my customers. Also, you say you are only planning to stain the top side of the boards but for best results you should stain all 6 sides of the cedar. If you don't want to stain the sides and bottom, make sure you definitely stain the end grains - VERY important.