SmartPro package differs from the regular Combo packages.
But actually the difference is not so big. So, 3d party mods can be installed without additional problems or site corruptions.

I admit that the corruption may happen during or after the installation of 3d party mod. This is due to that SmartPro has pre-integrated own add-ons already. They can be interfered with 3d party mods and corruption can be occured but with a very little percentage of probability.
My advise is to contact and consult see more first the developer of the 3d party mods if they can be used or already used with SmartPro package. Many of experts has worked with SP package and can speak for whether their mods can be used or not.

As for the Admin menu issue. We have experienced some bugs happening in IE. We have have fixed them in the today's release of the 6.0.0004 patch. We strongly recommend you to upgrade to it.