The current style of conversations we implemented is inspired by Gmail, so the order is currently only from the Oldest at the top to the Newest at the bottom. The messages marked as read will be collapsed by default so you will always be able to read the newest messages comfortably, but if you want to read the whole thread you can do so in a natural order.

The order currently CANNOT be changed, but it's being considered for the future versions of eM Client.