To mark foods in your meal plans as eaten, be sure you're on the Day view on your planner page. Here, you can check the boxes to the left of each food in your plan, which will mark those foods as eaten and display a new progress bar at the top of your plan. If you hover over the percentage eaten, you'll see an overview of the calorie and macronutrients you've eaten so far.

Using this option to lock meals in place:

Marking foods as eaten also works as a locking mechanism, so any checked items will stay in place when the meal plans are regenerated. You can use this option when you need to make some manual adjustments to your meal plans and want to regenerate the other foods around these. If you have set up a meal and checked this, you can then regenerate that day, and the other foods in your plan will be regenerated around the checked meals in adherence with your nutrition targets.

Just note that this option does also remove the ingredients for any checked meals from your grocery list, so you'll want to be sure to uncheck that prior to doing any needed shopping.