Onions behave like Krakka in terms of crossbreeding, so plant the onions with whatever you were using with Krakka to get the 2nd tier choco seeds, and you might be some of those.
As for what soil to use, rule of thumb is that if it's not a plant that has a static yield (glazenuts, thav onions, broombush, jute, minions, etc.) and you actually have a use for it, use Thanalan soil. I use Shroud soil only for Krakka and chocofruits (since I use those in bulk), and Thanalan for basically everything else as there's no point gardening if you're not constantly crossbreeding. There's always the small chance of getting 9x seeds from the Shroud-planted stuff at least.
