I'm biased, but I personally love S3 EP 6, "Race with the Demon" being the starting point ! It's already the iconic 2012 Jonatello episode for most who enjoy the ship and I think it's a great origin for their romantic storyline !
As cute as they are to me, I do think it would be better in the long run to have their relationship be a "slow burn" of sort / not get so heavily focused on they way April and Donnie were- I think it should be like a snowball gradually accumulating snow until it's undeniably clear ! So for example:
S3 EP 6, "Race with the Demon" : Showcases the most chemistry Donnie and Casey have had up until this point in the series, presenting as a simple kinship but leaving room for something more (To those looking for it at least-).
S3 EP EP 7, "Eyes of the Chimera": Further building on their new friendship status via their interactions, especially in stressful / high stakes scenarios (Like the Chimera situation-).
// Not necessarily an interaction thing, but I love Donnie sporting a mask in S3 EP 8, "Vision Quest" and I think it would've been cool to have that be such an obvious nod towards Casey from Donnie- Showing how much he's grown to accept Casey as his friend ! //
S3 EP 17, "Meet Mondo Gecko": Maybe Casey could've been texting Donnie at certain points during this episode, like before getting kidnapped by Xever / "Fishface", earning a reasonably concerned reaction from Donnie later on.
S3 EP 22, "The Creeping Doom" : Having Casey be involved in this episode, for starters- LMAO / Maybe Casey could be surprising cute with Donnie is his low IQ state, referencing the fact that he takes care of his younger Sister and knows how / when to be caring and gentle with others ! Also Donnie could experience a lot of embarrassment at the knowledge that Casey witness his like that- Causing Donnie to question the amount of importance Casey has in his eyes !
S3 EPS 25-26, "Annihilation, Earth!" : I know its kinda cheesy and cliche, but having those two admit that they've felt something more than friendship for one another in what they believed was their final moments together ! Just for Fugitoid to show up and save them, making that confession a bit awkward for them both-
The entire Space Arc could be filled with moments of them wanting to figure out what they are but finding excuses to avoid it,, Like, "Uh oh! Can't work through are potentially romantic feelings because a space shark that's also a bounty hunter is trying to kill us! Darn!", you know? I could also see them putting April in the middle of their stupidity because they're trying to seek refuge or normalcy between them,, Essentially running from their feelings because it's too much for either of them while on a Space race to save Earth,, (But it's not like that's fair to April either-)
S4 EP 22, "The Power Inside Her" : This should be the episode that they truly get together in my eyes. Casey almost lost Donnie once again, and in seeing him molecularly scattered, his feelings never felt more clear. So at the end of the episode, Casey confesses to Donnie in private (Maybe in Donnie's lab? Maybe on the roof above his apartment complex?). He's more vulnerable than he's ever been in his life, probably. Thankfully, Donnie would reciprocate ! Maybe even admit that he thought of Casey before getting molecularly scattered, and wasn't sure what to do with those feelings. It's a sweet / wholesome moment as it morphs into that still image ending 2012 loves to do at the end of episodes-
S4 EP 23, "Tokka vs. The World" : It's shown that Casey and Donnie have yet to share their new relationship status, but you get cute bits like Donnie winking at Casey affectionately before leaving him behind with Mikey inside TCRI !
S4 EP 25, "Requiem" : Relationship status is known by everyone else now. Maybe they make a joke or two about it? Donnie and Casey sitting close to one another as they watch the, "Chris Bradford's Too Ruff Crew" finale with everyone else- Maybe they have a moment where they try to hold hands for as long as possible before splitting up into groups after Super Shredder attacked the Mighty Mutanimals hideout-! Casey definitely comforts his grieving boyfriend post Splinter's death,,
S4 EP 26, "Owari" : Somewhere in this finale, they should have their first on screen kiss- I think towards the end of the episode would make the most sense contextually !
S5 would just be filled with fluff and whatnot, reaffirming that they're still a couple and still very happy ! 💜🖤