On the nesting parameters page of the wizard you have the ability to rotate the geometry any interval you wish. If you want to use the standard 90-degree setting you can or you can change it. The default value is 90 degrees. You can also use lower priority parts first to increase efficiency. You can re-nest your parts as well to get different results based off of your edits. What you are referring to as "issues" aren't actually issues but more what you told the software to do. You may want to review the Help system on the nesting wizard for assistance. Also, try positioning your original geometry in the lower left quadrant of the drawing screen so it doesn't interfere with your view of the nested sheet once produced.