You can run a CFW alongside a Sky3DS very easily, there's nothing confusing about it.
*for someone who reads stuff properly, which is pretty rare on the internet, even i mostly just skim stuff sometimes......how many times did we see "so gateway update supports 6.x so i bought it and its not working HALP!".....if someone was on 9.2 or lower it would be better to go with pasta or gateway.....i suppose if they have a second 3DS on 9.3+ then sky3DS might be a good investment, but really saying stuff like "sky3ds supports cia installs and 9.8" in the same sentence will probably confuse a lot of the usual victims who rush to buy and first ask questions later.
but for the OP i would suggest he just looks for a 9.2 or lower system and gets hold of a copy of CN/ocarina of time fore a few mins to downgrade MSET and use his gateway on the n3DS and his o3DS, if he is familiar with the setup and is used to it, really GW is still the best option for the n3DS, cartless bootup via MSET, emunand, xenoblade (which is probably one of the only real draws to the n3DS atm)