IIS 6.0 supports both the 32-bit mode and the 64-bit mode. However IIS 6.0 does not support running both modes at the same time on a 64-bit version of Windows. ASP.NET 1.1 runs only in 32-bit mode. ASP.NET 2.0 runs in 32-bit mode or in 64-bit mode. Therefore, if you want to run ASP.NET 1.1 and ASP.NET 2.0 at the same time, you must run IIS in 32-bit mode.
ASP.NET 1.1, 32-bit version

// To run the 32-bit version of ASP.NET 1.1, follow these steps:

1. Click Start, click Run, type cmd, and then click OK.
2. Type the following command to enable the 32-bit mode:
cscript %SYSTEMDRIVE%\inetpub\adminscripts\adsutil.vbs SET W3SVC/AppPools/Enable32bitAppOnWin64 1
3. Type the following command to install the version of ASP.NET 1.1 and to install the script maps at the IIS root and under:
%SYSTEMROOT%\Microsoft.NET\Framework\v1.1.4322\aspnet_regiis.exe -i
4. Make sure that the status of ASP.NET version 1.1.4322 is set to Allowed in the Web service extension list in Internet Information Services Manager.

ASP.NET 2.0, 32-bit version

// To run the 32-bit version of ASP.NET 2.0, follow these steps:

1. Click Start, click Run, type cmd, and then click OK.
2. Type the following command to enable the 32-bit mode:
cscript %SYSTEMDRIVE%\inetpub\adminscripts\adsutil.vbs SET W3SVC/AppPools/Enable32bitAppOnWin64 1
3. Type the following command to install the version of ASP.NET 2.0 (32-bit) and to install the script maps at the IIS root and under:
%SYSTEMROOT%\Microsoft.NET\Framework\v2.0.50727\aspnet_regiis.exe -i
4. Make sure that the status of ASP.NET version 2.0.50727 (32-bit) is set to Allowed in the Web service extension list in Internet Information Services Manager.

ASP.NET 2.0, 64-bit version

// To run the 64-bit version of ASP.NET 2.0, follow these steps:

1. Click Start, click Run, type cmd, and then click OK.
2. Type the following command to disable the 32-bit mode:
cscript %SYSTEMDRIVE%\inetpub\adminscripts\adsutil.vbs SET W3SVC/AppPools/Enable32bitAppOnWin64 0
3. Type the following command to install the version of ASP.NET 2.0 and to install the script maps at the IIS root and under:
%SYSTEMROOT%\Microsoft.NET\Framework64\v2.0.50727\aspnet_regiis.exe -i
4. Make sure that the status of ASP.NET version 2.0.50727 is set to Allowed in the Web service extension list in Internet Information Services Manager.

Ref : http://support.microsoft.com/kb/894435