After importing transactions you will see a red "Unallocated" button at the top. This indicates that you have transactions that have not been allocated to envelopes.
Click on that button an the "Unallocated Transactions" window appears. A list of your unallocated transactions is on the left and your envelopes are on the right.
Banks often give ugly and unhelpful descriptions to your transactions. You can change that by clicking on the "Edit" link that appears when you move your mouse over one of the transactions on the left.
Now just drag transactions from the left and drop them on top of the envelope they belong to. This is great for most transactions which go into just one envelope.
Sometimes transactions are more complicated and you may need to split them across several envelopes. In that case drag the transaction from the left side up to the "Split" area. A transaction editor will appear and you can split the allocations across as many envelopes as needed. Click "Save" and you're back on the main window.
You can also click to select several transactions and drag them all to an envelope at the same time.
Once the list on the left is empty, your budget is up to date. Click "Close" to hide this window and you're done!