Once you've built CS, you don't usually need to build it again. Anyhow, typing 'jam' a second time won't cause anything to be rebuilt since all the built stuff will be up-to-date already. If you are ready to create your own game, you usually want to install the built CS toolkit via 'jam install'. You can then use 'jam distclean' to clean up all the temporary build stuff, if you like.
To create your own project, you use the jamtemplate/createproject.sh script. This will set up a skeleton project for you which utilizes the built CS which you installed, so you normally will be building only your own project and linking it against the built CS toolkit. Since you are using the 0.98 release of CS, you will find the createproject.sh script in the CS/scripts/jamtemplate directory. If you move instead to the CVS version of CS (recommended), then you will find the script both at CS/scripts/jamtemplate and at the installed location ${prefix}/share/crystalspace/build/jamtemplate. For further instructions, for the CVS version, see the section "Creating an External Crystal Space Application" in the CS manual at
http://www.crystalspace3d.org/docs/online/manual/ (presently section 4.21.1). This HOWTO probably is also mostly applicable to the 0.98 release.