Sorry for the late reply.
The reason that we ask for the platform is that, by knowing this, we can supply you some out of the box reports without you having to do anything. This is what you see in Environment under default data reports. Knowing the platform ahead helps us collecting and parsing the stuff correctly and also enables us to present different reports depending on the platform you are using.
Using two monitors is not recommended but possible. You could not, however, make them report into the same project. You would have to make two projects. If the bulk of the functionality in your app lies in managed code I would recommend that you choose the .NET monitor. If not, i would recommend choosing win32 and call this from managed code as well using pinvoke.
EQATEC Application Analytics is now Telerik Analytics
. For more information on the new name, plus what's new in Telerik Analytics, please, check out the Analytics Service Announcement