No problem for me with relative paths to 2 C files in the same directory:

C:\>type a.c

void foo() {
 printf("Hello from foo\n");
}


C:\>type b.c

void bar() {
 printf("Hello from bar\n");
}


C:\>type try.pl
use warnings;

use Inline C => "./a.c";
use Inline C => "./b.c";

foo();
bar();

C:\>perl try.pl
Hello from foo
Hello from bar

C:\>
[download]

It may well be that relative paths need to begin with "./".

For LIBS and INC I think you do need to specify an absolute path which, for the cwd, should just be File::Spec->rel2abs('.')
And, yes, that would need to be done in a BEGIN block.

To me, that doesn't seem so bad - I guess it could always be improved.

Cheers,
Rob