When you add more geometry to these non-planer areas then you can easily end up with many more non-planer poly's which becomes more difficult to clear up. You can fix this when the model is still very simple by aligning the view from different angles and adjusting points one at a time until the area looks flat from every direction, once all that's done then start adding more geometry.
Now I also see several loop cuts that are really close together and this can exaggerate the non-planer issue because the thinly sliced quads can become overlapped. There are several cases of this happening here.
I think to start with, it's a good idea to test whether or not loops are too close by zooming out and making sure that you can still see a clear distinction between individual loops.
To help clear this up you can activate Edge Selection mode then use Alt+Click to select an entire edge loop and double tap g to slide the edges around until they are more even.
You may have also noticed that when you first create an Edge-Loop that you can slide it around before pressing Enter to set the Loop. Use this to control exact placement when creating them.
There are also many extra Loops in there that are likely unnecessarily because generally they are only needed close to the edges but not normally across flat surfaces between the transitions(I'm sure many people have reasons to do this but in your case I would avoid it for now until you are sure you need to do this).
Now to remove unwanted Edge-Loops, you can select a Loop using Alt+Click as before and press x then g. This will first open the Delete menu then activate the Edge-Loop delete function. This is a great way to clean up a model.