'Manually' probably means not using a package manager - either with the configure/make dance, or with a binary installer like Google Earth used for a long time. In those cases, you still need to sort out dependencies manually.
Absolutely; if the dependencies exist within the appropriate Ubuntu repositories, or the ppas you have active, then the needed libraries can be installed.
Random downloading of debs from Web sites could lead to a situation where a different version of a dependency is needed. "foo needs libnaff-ubuntu345 but libnaff-ubuntu345 is not going to be installed" type errors result.