Standalone TLB Side Panel?

1. My TLB menu in QL-Taskbar (W7-x64) is on sync with the new sidebar. Even I reorganize with hiding, everything goes back after a restart.

TLB saves all settings and shortcuts in the toolbar folder. When you've opened the standalone TLB, it asked you for toolbar folder. I guess you've selected the default folder. There are two ways to fix this:
* The first way:
TLB Settings->Options->Toolbars. Create the folder somewhere on the disk and add it into the toolbars list. Now you can switch toolbar folder via right-click->Switch Toolbar

* The second way:
Right-click the standalone TLB (empty space) and select "Close toolbar". Run the Standalone TLB again and press the "Select folder..." button to select the other folder.

2. Although necessary plugins installed, I have some problems installing new skins.

Here is the guide for skin installing. If not helped, please let me know what skin you install.