Any multiple desktop creating component available?

I am developing a VB.NET application that sends windows messages to another windows application and therefore behaves like a data entry operator. I am using SendKey.SendWait() method to do the same. The limitation of this method is that it sends message to the application that is on the foreground of the desktop, i.e., an application which is active on the desktop to receive inputs from the keyboard.

The problem I am facing is that I may have to develop my application such that it sends messages to multiple instances of the receiving application. Using win32 APIs I can always 'activate' the recieving instance before performing the 'SendKey.SendWait' on it. But I guess this will be a little messy.

Now I am looking at two approaches:
One is to send message to the application using the handle of the window. I use the SendMessage win32 API. This however is a little difficult to code for variety of messages to be sent to various windows child controls. I am ready to explore it further with any easier suggestions.
Second is using the multiple desktop approach. There are plenty of downloadable applications on the net that make various instances of the desktop. I can switch between desktops and have seperate applications running in different instances of desktops. If I can have such multiple desktops then I guess I will be able to have one active application on each of this desktop instance. I hope my direction is right.

What I am expecting from the forum is the guidence on the first approach and some directions on the second. I want to know if the second approach is viable at all and if yes, then are there any components available to include in my applications that can make multiple desktops (I have downloaded 2 applications but no pluggable components to be seen).

Regards,
Daljeet