You should uninstall the installed version first completely with sudo apt-get remove bitcoind before manually building the binaries from source. Make sure that you backup your wallet (and eventually Blockchain) first (so Keep your data-directory).
Don't run the build in teh bin folder! The sudo make install command will install more than just the binary on your machine! Use e.g. /home/git/bitcoin/ to clone the repository and run your configure and make commands there.
Then instlall bitcoin like described on github. after your make -j2 command you should run sudo make install to install bitcoind on your computer. (Binaries are intalled under /usr/local/bin/).
I have installed it on my raspberry Pi a week ago. Works fine :-)
Blockchain-sync lasts almost forever ....
If didn't use the --disable-wallet flag. You could use the wallet with bitcoin-cli