If you’re going to install from source at least change the compile config options so the prefix defaults to /opt/program-name.
You can further integrate with the system by adding the /opt/program/bin/ and sbin/ dirs to the PATH variable, and add lib/ to /etc/ld.so.conf but it should not be needed normally — only if other programs need to compile against this one.
You can also simplify integration by making common dirs for example /opt/.bin and /opt/.lib, adding only those to PATH and ld, and symlinking binaries and libraries from all /opt programs to them.