PuTTY is compatible with the Desktop Agent and is available from https://www.chiark.greenend.org.uk/~sgtatham/putty/latest.html.
You should be able to use PuTTY without any additional configuration after you have installed the Desktop Agent. The only requirement is that you have the "Attempt authentication using Pageant" set in the Connection -> SSH -> AUTH section of the connection dialog. This is normally set by default for new connections.
PuTTY supports its own "pageant" process which does not implement access through sockets or named pipes. It uses a form of IPC and therefore requires the use of a proxy program that we start when the Desktop Agent launches. This program translates from the PuTTY IPC mechanism to the Windows named pipe supported by Desktop Agent. It is simply a modified version of the pageant application supplied by PuTTY.
Unfortuatley this means that you cannot run the standard Pageant utility at the same time as the Desktop Agent. If you start the Desktop Agent and Pageant is running you will receive the following error. It will not stop the Desktop Agent from working but will prevent PuTTY from using the Desktop Agent keys.
If you see this error you should close down the standard Pageant process and restart the Desktop Agent.