This is very tricky, even trickier it is in cross development environment. sdl-config is by default provided by host, i.e. it points to host libraries. So when using m68k SDL, you first have to alter PATH for application's ./configure. But you can't set it forever, because it clashes with tools like m68k 'as' which got installed into <prefix>/bin along with m68k sdl-config.
With multilib, it's stupid manual overriding, personally I use only -m68020-60 builds, so I configured SDL with --libdir=<prefix>/lib/m68020-60 and therefore my sdl-config points there. For multilib environment this must be one big mess and very painful thing to do.