Yeah, I didn't see this thread anywhere so thought I'd make one myself.

How would you have these two meet in your head canon?

For mine, Twilight and Flash met in kindergarten and became good friends, along with Sunset Shimmer and Trixie Lulamoon. They all stayed good friends throughout school until a rumor went around about Flash that caused both Twilight and him to get into a massive argument, resulting in them never talking again for a few years. During that time, Twilight began to study under Princess Celestia (still working on what) and Flash joined the Royal Guard. Sometime after Twilight became a princess, the two met again in Manehatten and caught up. Twilight asked Flash to escort her back to Ponyville where Flash explained about that rumor and Twilight apologized for believing it. She explained that she tried to find him after the fight but couldn't find him anywhere. Eventually, Flash was transferred to Ponyville and became Twilight's Personal Guard and later boyfriend. They later married during a war that took place two years later.

man that's a mouthful of writing.

4448924 Basically how they met in canon. With the exception of Rarity and the rest of the mane six(sans Shy ad Dash) playing match maker.

Shy and Dash weren't too keen on the idea of their "brother" hooking up with their new best friend(especially Dash). When the two did begin dating, Dash was very ambivalent about it. Believing Flash's bad luck when it came to mares would strike again, and he would be hurt by this. Luckily no such event came.

Shy warmed up to the idea of the two dating faster than Dash did. Eventually, the two started referring to Twilight as their sister.

Everything else can be found here. Though, it's mostly about the human counter parts.

For me, the mane six set up the two, but things don't go exactly as planned. After some explaining the two rescure Rarity, yadda yadda... I was new at writing...

4448924 Equestrian Twilight falls in love with Human Flash, but can't stand Equestrian Flash, even though he constantly hits on her. So after an unfortunate 'accident' during one of Shining Armor's Training regimes, Equestrian Flash is dead. Human Flash confesses his love to Equestrian Twilight and agrees to travel with her to Equestria after graduating high school. They lie happily ever after in her Castle, raising a teenage brat who's ego is to big for her to handle and a young shy colt who is crushing hard on Pinkie Pie's daughter, who is most likely named after something sweet and sugary.

4448924 Inspired by her future sister-in-law, Twilight started working as a foalsitter for a little filly named Scootaloo, when she noticed that her older brother Flash was kind of cute. And so history repeated itself.

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Extensive meddling from Cadence and Shining.

4448924 A scheme hatched by Cadance after seeing how Twilight kept staring at Flash a bit more often than usual and co-conspirators were nearly everypony of Twi's friends save Spike and Shining Armor. Spike because he's too young and not interested and Shiny because... well, he's not too keen on hooking up his sister with somepony else. Nonetheless, he doesn't interfere.

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How would I prefer them to meet or how do they meet in my story?

In my story, the meeting happens when some strange ponies arrive at Ponyville, looking for another strange pony who helped Rarity. Twilight then sends a report to Luna, explaining the situation and in the next morning is surprised to see that Luna's response consists of a platoon of guardsponies. That's how she meets Flash.

As for the relationships, there is no attraction between them at first, because their minds are focused on something else.

My headcanon varies a little. In my 'Marriage of Celestia and Discord' series, Twilight encountered Flash at Celestia and Discord's wedding where Flash asks if he can become a guard at the Castle of Friendship, with Twilight making him captain of the guard.

In a different story I'm writing, Flash was assigned as Twilight's captain of the guard by Princess Cadence, which may or may not have been a coincidence.