Hello,
You can change positions of logo only to corners or center position. If you want to have logo inside graph, there are 2 possibilities:
1. Use Flash settings and upload there logo with right and top space to move logo out of flash borders. This space should be transparent. It has 1 negative, logo can have link and this space will be part of link too.
2. Do not use flash settings, but upload logo to article. Div around flash needs css 'position:relative;' and logo inside that div needs 'position:absolute;'. Then you can place logo where do you want.
Flash is normally top positioned and you can't see div or any other html element over it. If you will have this problem with example 2, let me know and I will tell you what you need to change.