If you have autolayout turned off you should be able to select any box and
drag it to where you want. Are you sure that autolayout is "deselected"?
Or, if by long lines, you mean that they are connecting to the sides of the
boxes, you can select the line and then click and hold on one of the little
red circles and move it to a different node on the box.
You can "escape" from Org Chart and then have all of the drawing tools and
other functions in PowerPoint. As a safe experiment, insert a new blank
slide using the "Title Only" layout. On your current slide select the Org
Chart and within the boundaries, drag the cursor diagonally from the upper
left corner to the lower right corner to select all of the boxes, lines and
text. Press Ctrl + C to copy. Go to the newly inserted slide and press
Ctrl + P to paste everything. Now you can modify it anyway that you want.
If you find that that mode works best for you, you can delete the original
slide.
