This may be coming a bit late for you, but I ran into a similar issue. In my case, I needed a Fortran compiler (amazing, right?), but that was not included by CodeSourcery.
I set up my BSP to run in Ubuntu 15.10 and installed arm-linux-gnueabihf-gcc. Note that Ubuntu 16.04 did not work for me, sadly, because the kernel supported by LogicPD was too old for the compiler. Then in the LTIB configuration, I set it to use the C library package from my toolchain only. I also set the toolchain to "custom". The path is "/usr". The prefix is "arm-linux-gnueabihf-". My CFLAGS are "-O2 -fsigned-char -std=gnu89".
Rebuilding the image was a bit of a chore, particularly because the newer compiler's default GNU dialect is std=gnu11, which is a change from the older gnu89. I ended up removing many packages from the build due to compile errors. I fixed the errors for packages that I did need. I couldn't quite get the u-boot compile to work, so I just used the binary u-boot provided by logicpd.
Things seem to work for me now. It's also nice that anyone with Ubuntu 15.10 can build for my system. The Fortran compiler was critical for our work, and that seems to be working so far.
I hope this helps!
~Mike Foss