Most experienced users will suggest leaving fillets to the end of the feature history. This is not always possible. Some general filleting tips I use:

1. If I have to fillet the edges of a face, and I then need to put a sketch on the same face, I will make a workplane first that is offset 0 units from said face. This allows me to more easily add, delete, and change the fillet without worrying about the sketch on the face reacting "badly."

2. If a round is so important to a shape to need to be put early in the history, I put it in the sketch, and avoid using fillet features.

3. I use the "loop" and "feature" fillet select options as often as possible. They react better to radical design changes.

4. Once a model's functional shape is done, I start with the largest rounds first, then move my way down. This not only makes the feature tree organized and predictable from one model to the next, it can also increase the chances of a tough round working the first try.

5. If you find a vertex where multiple rounds come together, try doing this in one fillet operation. Remember that the fillet dialog allows you to mix multiple constant radius fillets and multiple variable radius fillets in one feature.

6. For cast parts with many rounds, I avoid turning off the "Rolling ball" option. Rolling ball fillets are spherical. Non-rolling ball fillets are n-sided patches (good for consumer products and aesthetics). Why does this matter? ASM is much faster working with the "Rolling ball" fillet type.

7. In very tough fillet cases, ones where no-matter how you try to fillet it does not work, try turning off "Automatic chain edges." Fillet the edges that are important first then come back and pick up the remaining edges in another fillet. This technique has allowed me to fillet many models considered unfilletable...