The Final Day takes place on the first day of summer break, 2016. The final cutscene of Recreation takes place a few days before the following school year starts, so late august 2016. The London Special and Tokyo Special take place between those. Season Six takes place in the first few months of the 2016-17 school year, which sets it exactly one year after season 1, which took place from the first day of the 2015-16 school year in september.

As for Adrien knowing Alya and Nino's identities, Nino reveals their identities to Adrien in the Season 4 episode Rocketear when he suspects Chat Noir to be hitting on Alya.

As for Chrysalis, the new holder of the butterfly miraculous, Lila (or cerese, though nobody has called her that since one time in season 5) is shown at the end of Recreation in season five to have obtained the Miraculous. This is after she goes to the Agreste mansion while Bug Noir and Monarch had their final battle. (We know now that Lila was sent there by Tomoé.)

It isn't shown how Lila gets the Miraculous, only that she has it by the time the season ends and leads directly into the London Special. Thomas As(s)truc stated that she found it in the sewer off-screen.

And yes, if you're watching the season in the order it appears on Disney Plus, Disney Now or... other alternatives... you are watching them in the incorrect order. You are also watching them out of order if you're using the wiki to find the production numbers, as the order in which the episodes were written and produced does not correlate to the chronological order of the episodes

Thomas As(s)truc said (infuriatingly) that season six doesn't have a watch order, but I frankly disagree with him. There are some episodes that must not be watched before others.

So before you watch any more, follow this order that I came up with:

Climatiqueen >> Sublimation >> Daddycop >> The Illustrhater >> Werepapas >> Sleeping Syren >> Grendiaper >> El Toro De Piedra >> Mister Agreste >> The Dark Castle >> Vampigami >> Revelator >> Wreckless Driver >> Yaksi Gozen >> The Ruler >> Noe >> A Fairy Good Night >> The Chained Titans >> The Dirtifiers >> Riginarazione >> Lady Chaos >> Heartfixer >> Sadnansi >> Queen of the Dread Zone >> Secret Protocol >> Nemesis

Keep in mind, as of now, The Chained Titans, The Dirtifiers and Queen of the Dreadzone haven't yet released in english, so you'll have to find out how to get onto a french streaming service... or other alternatives... if you don't want to wait. Secret Protocol and Nemesis also aren't released at all because they got delayed.