Multiple different configured projects in one dir

[LCID Fire]

I have a autotools build which generates a few binaries - and one being 
a sort of compiler - so I'd probably need to configure this one binary 
with the --target parameter.
My questions are:
Do I need 2 seperated builds to achieve this or can I change the target 
for one binary in particular.
When I need 2 builds - is there a way to link them together (to ease 
configuration/compilation)?