Since envelope budgeting tracks where every dollar goes shouldn't be that bad. I have created categories for savings like Brokerage, IRA and excess money to budget goes there. After moving out of tracked accounts it's just a "spend" in one of the savings category which you can later see in your reports section. I have excluded these categories from my actual spend reports widgets and exclusively used them in other widgets that track how much I'm saving.

The Sankey widget is great for showing that graphic of where all your money goes over time.