SmartSelect will ALWAYS pick better channel assignments than a static channel assignment. It basically works by trying every single channel constantly and remembering the max throughput on each channel. Then it stays on the channel that it knows has the best capacity.
So, if you only have 3 AP's with heavy traffic, they will all stick on 1,6,11. But in reality, one of those channels will likely be noisy due to either non-802.11 sources of 2.4GHz interference or someone operating another 2.4GHz access point. So the conventionally "recommended" 1, 6, 11 might be a bad choice. In fact, if you are deploying in a rogue environment where everyone else chooses 1, 6, 11, then those might be the WORST channels. The overlapped channels might actually have more capacity than 1,6,11.
The main downside with SmartSelect is that it can take a few hours for it to stabilize because it is essentially exhaustively trying every channel to establish how much capacity it has. Not all clients support the 802.11h channel change announcements (CSA) that Ruckus sends. Those clients may be dropped off the network every time a channel switch happens. If this is an issue in your environment, there are two solutions:
(1) Use the CLI to change the channel fly MTBC (Mean Time Between Change) to something higher than the default 100 minutes. This can reduce the amount of disruption.
(2) Use ChannelFly for a few hours to establish the best channels, then manually set those channels. If you have a ZoneDirector, it can automate this process by you selecting the "Stop Channelfly after ___ minutes" option. If you're standalone, you should run ChannelFly for a day, then log into the Web UI and see which channels the AP has picked for 2.4 and 5GHz, then manually set those channels.
The downside of approach (2) is that you cannot dynamically react to changes in capacity. So if someone happens to bring in a rogue AP that uses the exact same channel you are using, you'll have to manually diagnose that capacity loss if it becomes an issue.
For your second question, I think the answer depends on your goals. Are you still evaluating, or are you now using the Netgear AP to add more wifi coverage in addition to the Ruckus AP's? In a standalone environment roaming is done purely on the client side, so the client won't know what's a Ruckus and what's a Netgear. But having a mixed environment like this will make it much harder for you to diagnose what is wrong if someone complains about wifi performance/connectivity.