Your backfoot does an amazing job of following what the board and front foot just did. If you're initiating the turn with your front foot using torsional flex, the board is going to carry that "twist" to the backfoot. It kind of goes along with the situation. Just don't resist it. You're right you will be flat based for a brief period. This is important because it makes that edge change smooth and easy. Trying to change edges while skipping the flat based portion is often how you catch an edge.
To answer your question, once your front foot has gone flat based, you can begin to pressure it to the new edge. Again as long as you aren't resisting with your back foot, it will flatten out and then follow along to the new edge. Think of it like a wave. What you do with the front moves like a wave to the back. The wave in the back doesn't have to end before the next wave begins.
Another important thing to remember is to quiet your brain. You've only got 4 days in. Linking turns will develop. Just keep practicing and try not to over think it. Analyzing your every movement is the instructors job, not yours