I'm start to develop modules for DotNetNuke. I followed different tutorials(most by Chris Hammond) but there is something i don't like, and I'm searching a different way to do so.
He recommends to put a DotNetNuke installation, with IIS and SQL Server, on the developer PC and put your Project into the DesktopModules folder. I don't like it because i want to separate my project from DotNetNuke.
Is there a way to split the build/publish to different location like dll into folder x and all other stuff into folder y?
You could, but I don't really see the point. I see where you're coming from because it seemed awkward to me at first as well, but it really is the most efficient way to develop on the DNN platform. I have mine set up so all of my modules are in the same solution and branched in source from the root DNN folder. We don't keep the DNN core in source so the developer is responsible for that, although that may change at some point to keep versioning consistent.
By keeping your project located where it's installed, you can develop your modules the same way you'd develop any other web app you're building. If you make a change in markup you just have to save the file and refresh your page. If you change something in code just build and refresh.
If you really must keep them separate, you can absolutely do so (really the only benefit of this that I can see is that if you uninstall a module and accidentally click the checkbox to delete files - it happens - you don't have to worry about it). Create your project where you want it, change the Output Path to your DNN bin folder, and create post-build events to copy all of your .js, .ascx, and .css files (plus any others you may need - images, HTML files, XML files, etc.) to appropriate folder(s) in the DesktopModules folder. Just remember that you have to build the project every time you make ANY changes to test them, and you have to write/change your post-build events every time you add a new type of resource, change/add a directory, etc.
Either that or you can build an install package and uninstall/reinstall the module every time you change some padding in your stylesheet ... but I'd stick with keeping the project in the DesktopModules folder.