Eclipse adding your own build command

In addition to what smeg4brains said and assuming that you are using the CDT plugin you can go to:

project -> properties -> C/C++ Build

Uncheck Use default build command on the Builder Settings tab and replace make with e.g. scons.

On the Behaviour tab you can then specify the target to call for the Build and Clean phase.

To resolve your second issue open the Project menu and uncheck Build automatically. This will prevent Eclipse from building the project when it thinks it is necessary.

You can add a custom builder in the "Builders" category of the project properties.

project->properties->builders->new

there you can also deactivate the default eclipse builders..

hope that helped