Where Can We Use Our Custom Decks?

Cockatrice has no rules enforcement/automation, you're thinking of something like Xmage or Forge where every card has to be coded to act like it would in MTGO/Arena.

Current versions of MSE should come with a Cockatrice Exporter that will let you export a plugin that you and other players can use. Note that you will have to share the images with them as well unless you edit the plugin file to support images you've hosted on a site like imgur. For more detailed assistance I would join the Cockatrice Discord and asking around there.

If you want to find people to play custom cards with on Cockatrice, I believe their Discord has a custom cards channel for this sort of thing.

For Tabletop Sim, when you make a custom card you will have to provide two image URLs. One is a URL to a card back, the other is a URL to the card 'front', which you'll need to have uploaded to a site like imgur. You want urls that end in image extensions like "jpg" or "png" for this to work, for exmaple: gamepedia.cursecdn.com/mtgsalvation_gamepedia/f/f8/Magic_card_back.jpg

Once you've made custom cards/custom decks, you can right click on them and save them locally for future use.