I wanted to submit a run of all minigames from the dsiware version of the game. Would I submit this as a new game or submit this under the DS category?

https://plantsvszombies.fandom.com/wiki/Plants_vs._Zombies_Nintendo_DSiWare

There are variables for every main category: PC/Console/DS. So you just choose a respective category (Mini-games) and submit it there specifying that it's a DS variable

How do I specify that?

Just submit a run, you choose the platform there along with any other information about your run. Button "Submit" is in the top right corner on the game page