Iku, you can choose whether you want to cycle the 46 or not.
As Agu suggested you can setup the 46 just like any brand new tank and let it cycle for a couple months then think of your 12g as a fish store

it's the place you go to get livestock for your 46.
If you'd rather not keep 2 tanks up for so long you can also set up the 46 with just powerheads, heater, water and substrate and then move everything (including the water) from the 12 into the 46 as soon as it is up to temp. You will essentially have a 12 gallon tank in a 46 gallon enclosure. As long as the new substrate doesn't have any biological detritus in it you won't see any kind of cycle. If you get live sand it can be problematic because there will undoubtedly be die-off which will cause a cycle.
The only problem with this approach is that you will have to be careful about adding liverock. It will have to be fully cured live rock. I like this approach because you can buy really nice large pieces of mushroom rock, gsp rock, zoanthid rock etc. to make up the additional LR you want in the 46. You cannot add uncured or base rock to the tank it will cause a cycle!
You are able to do this because you are not adding any biological load to the bio-filtration that your currently well balanced tank has. It is important that the 46 doesn't have anything in it (ammonia, detritus in re-used sand, biological die off in uncured or partially cured live rock etc.) that would upset this balance. The additional water and the glass itself will quickly colonize with bacteria and the substrate will colonize pretty quickly.
The other risk is if you have a really dirty substrate in your 12 this getting stirred up could unbalance the biological load in the tank.