To some extent it depends on what you want to TT for:
Here's a good post explaining what to do if you want to go ahead a month to improve your grass and then go back to current time:
http://www.gamefaqs.com/boards/997811-animal-crossing-new-leaf/71804826
With beautiful ordinance and a 'locked down' villager (as explained in the link) you can move ahead safely in one jump.
I freeze time to play evey ingame day, tho I can't play much in RL.
I use the 3ds clock in settings to change the date & time to a time after I last played, load the game (which takes the time from the 3ds) & play.
I don't go back over a past save, all is as it should be, although I am in the past.
You don't have to be on correct time to obtain DLC, NZone DLC or to sell turnips in another town.
If you are playing other games where the time is important then you might be better to change time with Isabelle at the front screen of the game - this means that the 3ds & the ingame time will be different (& will remain different unless you manually change them to the same time using a 3rd outside clock that has seconds).
I've always changed time on the console- I don't play other games & I find it less confusing this way - but each to their own.
Edit: TT doesn't effect things such as built PWP - they remain.
Be careful TT around time related upgrades - the store & LOL club opening (I've seen no problems reported for the store, but I have for club LOL)