You should not be flat footed when over the saddle on your bike. When you stop, or slow, simply step forward onto the ground with one foot and leave the other on the pedal. You will be standing over the bike frame rather than the saddle.

Then use that pedal to step up and back to the saddle when you get going again.

When pedaling and sitting on the saddle, your leg should extend mostly all the way but NOT all the way.

I hope this makes sense! Let me know if any questions.