Setup:
  1. Install Cockatrice.
  2. Download 17.m17.xml.
  3. Import `17.m17.xml` via Cockatrice menu bar → `Card Database` → `Add custom sets/cards`

Deckbuilding:
  1. Paste your booster contents into a text editor and save as a *.csv file, then open in Excel. Or, paste directly into Excel and do `Text to Columns`.
  2. Sort by columns A then F then B then E, where E is a reverse sort.
  3. Track the cards you're maindecking by typing `1` in column G. You can highlight the column and look at the sum to get a count.
  4. When you're done, sort by column G, then highlight only column D of the cards you're maindecking, and copy-paste into another text file. You can add sideboard cards by prefixing `SB: ` like `SB: 1 Elixir of Memories`.
  5. Save your text file in Cockatrice's decks folder. For me it's `C:\Users\Xom\AppData\Local\Cockatrice\Cockatrice\decks`
Sorry there doesn't exist a better deckbuilding interface that supports custom cards.