One of the quickest and easiest ways to achieve smooth marker strokes when filling large areas is by masking the borders. Once the borders are masked off you are free to fill the area quickly avoiding the blotchiness that occurs when you work slowly with markers.
Masking can be achieved a few different ways. The most common is with masking tape, however it's not necessarily the best because masking tape can be difficult and time consuming to manipulate. There is also the added risk of damaging your artwork due to the adhesive lifting color or tearing your paper.
Luckily there is a better option that's inexpensive and can be placed, used, and then repositioned quickly.
Post-it notes are perfect - sticky enough to not move around, yet not so sticky that they can damage your drawings. Post-its are also just thick enough to for a few reuses before the marker pigment will soak though to your artwork below.
Give them a try next time you need to fill a large area of your drawing with marker.