You can install CLC software anywhere on your machine you have appropriate permissions for.
The location you choose to install Workbench software does not affect user-specific settings such as configured data areas or viewing settings, as these are held within a user's home area.
 

Points to consider when upgrading a CLC Workbench installation:

Upgrading within the same major release line

Here, it is generally best to upgrade in place. That is, install the new version on top of the existing Workbench installation in that release line. (e.g. version 10.5 of the Genomics Workbench would be installed into the folder where version 10.0 was previously installed.)

When updating CLC Workbenches within a given release line, you will be prompted to specify whether to install to the same folder as you previously installed to, or whether you would like to install to a new location.
If you are not sure where you previously installed to and would like to check, then just choose to install to a new location. The old location will appear as the default, and you can then proceed to install to that location if you wish.

Upgrading to a new major version line

Please install the Workbench to a new location. Installing to a new location is the default behavior in this case.
Please do not choose to install on top of an existing Workbench in an older release line.

When updating Workbenches of different lines (e.g. Genomics Workbench 11.x when you previously had Genomics Workbench 9.x installed), the default installation location is to a new area. For example, on Linux, the default location for version of the Genomics Workbench in the 10.x line would be something like:

/opt/CLCGenomicsWorkbench10

whereas for releases in the 11.x line, it would be:

/opt/CLCGenomicsWorkbench11
 

When upgrading to a new major version of the Workbench, you will also need to upgrade your license file.  How to do this is described in the manual starting at:
http://resources.qiagenbioinformatics.com/manuals/clcmainworkbench/current/index.php?manual=Upgrade_license.html

The same license upgrade information pertains to all CLC Workbenches.
To install software to a central location on your system, you will generally have to run the installer as an administrative user. Please see the related FAQ page for how to do this on your system. 

Description of a Major version or Major Release Line

"Major version" or "major release line" refers to the first digit in the version number. A minor release or bug fix release refers to the digit after a decimal point in the version. For example:

CLC Genomics Workbench 10.0.1 and 10.5 are different minor releases in the same major release line. The major release number here is 10.
CLC Genomics Workbench 10.x is is part of a different major release line than 11.x because the major version number is different (10 versus 11).