Packaging a CMake project (libRocket) into a .deb, but build script is in a sub folder
Solution 1:
The debian/rules file is the script that runs the build process. You can tell it that the build script is in a sub folder by passing --sourcedirectory=Build So your's might look like:
#!/usr/bin/make -f
%:
dh $@ --buildsystem=cmake --sourcedirectory=Build
See the manpage for the dh command 
for more information.