<p>I have a little dilemma on how to set up my visual studio builds for multi-targeting.</p>

<p>Background: c# .NET v2.0 with p/invoking into 3rd party 32 bit DLL's, SQL compact v3.5 SP1, with a Setup project. 
Right now, the platform target is set to x86 so it can be run on Windows x64.</p>

<p>The 3rd party company has just released 64 bit versions of their DLL's and I want to build a dedicated 64bit program.</p>

<p>This raises some questions which I haven't got the answers to yet.
I want to have the exact same code base.
I must build with references to either the 32bit set of DLL's or 64bit DLL's.
(Both 3rd party and SQL Server Compact)</p>

<p>Can this be solved with 2 new sets of configurations (Debug64 and Release64) ?</p>

<p>Must I create 2 separate setup projects(std. visual studio projects, no Wix or any other utility), or can this be solved within the same .msi?</p>

<p>Any ideas and/or recommendations would be welcomed.</p>

Not sure of the total answer to your question - but thought I would point out a comment in the Additional Information section of the
SQL Compact 3.5 SP1 download page
seeing you are looking at x64 - hope it helps.
Due to changes in SQL Server Compact
  SP1 and additional 64-bit version
  support, centrally installed and mixed
  mode environments of 32-bit version of
  SQL Server Compact 3.5 and 64-bit
  version of SQL Server Compact 3.5 SP1
  can create what appear to be
  intermittent problems. To minimize the
  potential for conflicts, and to enable
  platform neutral deployment of managed
  client applications, centrally
  installing the 64-bit version of SQL
  Server Compact 3.5 SP1 using the
  Windows Installer (MSI) file also
  requires installing the 32-bit version
  of SQL Server Compact 3.5 SP1 MSI
  file. For applications that only
  require native 64-bit, private
  deployment of the 64-bit version of
  SQL Server Compact 3.5 SP1 can be
  utilized.
I read this as "include the 32bit SQLCE files
as well as
the 64bit files" if distributing for 64bit clients.
Makes life interesting I guess.. must say that I love the "what appears to be intermittent problems" line... sounds a bit like "you are imagining things, but just in case, do this..."