I'll try to be more clear.
You can ignore the error and develop on the FreeCAD.exe but this is in Release mode.
If you want to attach FreeCAD to a debugger, you will want to compile FreeCAD_d.exe.
I think it's pretty common to have multiple build directories present at the same time. For instance, one build directory for master and another for your topic branch.
As far as copying the dependencies, it depends how concerned you are with disk space. The CMake switches are pretty bullet proof, but aren't very efficient. They copy a lot of unnecessary stuff. If you have multiple build directories you end up with multiple copies of the same stuff, not to mention they are already in the Libpack.
FreeCAD is designed to run from the build and/or the install directory. I think most, if not all, developers use the build directory and don't even run the install project. The build directory, directory structure is the same cross-platform. The INSTALL project copies files from the build directory and re-arranges the directory structure to match the target platform. The INSTALL project also doesn't copy some stuff from the build directory that is only necessary for compilation. The install project is mostly for distribution.
For an IDE, I guess MSVS-CE is probably the most popular on Win but people are also using;
QT Creator
KDevelop
Code::Blocks
It's personal preference. Some don't use the MSVS IDE because it is proprietary.
QT Creator, for instance, integrates well with QT, I here it integrates more seamlessly with other QT development tools like QT designer. It's opensource.
The FC-build.bat is probably something I posted on the forum? I haven't posted it on the wiki because it is not very general. If you want help modifying it for your needs I'm available.
I hope this is more clear.
And welcome to the project! It's always great to see people interested in developing FreeCAD. If there is anything I can do to help please reach out, PM if necessary.