Same issue here. In Joomla 3 the sidebar 1 moved to the left side when updating the ja_simpli template to version 2. (Main content -> content position is set to "left").
Using sidebar 2 and moving all content to position 5 indeed seems to work, but it is unclear to me then how the sidebars are organized.
Suggestion: make 3 options for Main content -> content position:
- right --> both sidebars on the left side, content on the right side
- middle --> sidebar 1 on the left side, content in the middle, sidebar 2 on the right side
- left --> content on the left side, both sidebars on the right side
That would make is very flexible, and logical.