Hi,
I don't really recommend using the "deployment" packages for development, those are pre-compiled and intended for production deployment.
What I do is main development in VS 2010 on Windows, but I have a separate set of projects and solutions for Mono (mojoportal.mono.sln) and I use those on Linux with MonoDevelop to compile packages for Mono. I know they have some Mono tools for VS but I never use that myself. I use VMWare Player and I download the latest Mono VMWare image, I use Hg to get the code and then I open the mojoportal.mono.sln solution in MonoDevelop and compile it there and test it there. I don't often test mod_mono, usually I just test test using xsp2 from the command line. In theory if it works in xsp2 it should work fine in apache with mod_mono, but historically there have occasionally been bugs in mod_mono.
I don't know anything about mod_aspdotnet and I never use apache on windows.
The main differences between the Mono version of projects and solutions is that we leave out some things like WebParts which is not implemented in Mono, and we also depend on Mono.Web for a helper class that handles things listed in Web.config that are not supported in Mono. So while I can open the mojoportal.mono.sln in VS 2008 and add files as needed, I never compile it on windows because I don't have the Mono tools installed. I just push changes to the repository and pull them down on the VMWare image to get the latest code on my Mono machine.
There is also some conditional compilation used here and there to work around Mono issues or things not yet implemented.
When I produce deployment packages for Mono, basically what I do is first produce a package for windows, then I compile in release mode on Linux using MonoDevelop, and then I replace the dlls in the bin folder with the Mono compiled versions.
There are bugs and issues in Mono, your mileage may vary using mojoPortal on Mono, I don't really recommend it for important production sites.
Hope it helps,
Joe