Yes, you are correct. In most cases visual properties of a RadControl can be modified in both ways.
And yes, it is possible to change visual properties with code. The best way for this is using behaviors.
For an example with behaviors, please see the following KB article:http://www.telerik.com/support/kb/article/b454K-thd-b454T-ckd-b454c-ckd.aspx
If you want to make a simple change (for example - change a background color) it is more appropriate to do it with code. However, if you want to set a few properties or if you want to make changes based on a condition, then it is better to create a custom theme.
Unfortunately, the background of the scroll thumb in RadPanelBar cannot be easily changed with code.
Also, it seems that you want to change multiple aspects of RadPanelBar's visual appearance, so I would suggest that you create a custom theme.
Contact us again, if you have any additional questions.
the Telerik team