There are a lot of old posts on here as there has been discussions before about whether or not it's a smart alternator. If you are interested do a search on the topic but it's pretty dry reading
A smart alternator is one that will cut in and out as needed to keep the start battery charged.
The reason it does this is to take load off the engine and theoretically save fuel.
The Wrangler's alternator just slightly varies the charging voltage via the onboard computer but it doesn't fall below 14Vs.
A smart isolator ensures that the start battery doesn't fall below 12.8V ensuring that it will always be able to start the engine.
Yes a deep cycle battery does require a different charge rate which is why you need a DC-DC charger for a smart alternator but with a standard alternator, because the voltage doesn't vary a great deal it's not going to hurt your second battery.
Most owners of smart alternator vehicles get their dealers to change to standard ones via the computer software so they can have a simple set up.