There are some established design patterns and conventions you can refer to, but they should just be references. Ultimately, your users goals and context should dictate these decisions. Context of use is everything; the way a user approaches your system to complete their tasks will dictate where you will need to place elements on the page. Consider forming a hypothesis and building a prototype to test with users. Don't lead them on, be as neutral as possible, and they will provide you with some answers. If you don't have the budget for this type of research, do a competitive analysis of similar systems and products; where do they place their elements? I would refer to heat maps and gaze plots for other similar systems if you can. Let me know if you can provide me with any more information about your systems and your users.