Can you give me an example from the batch file?
If i understand it correctly, you have added this compiler command for every file?
I think it would be more easy to generate a new compiler:
1) Settings->Compiler->Global compiler settings->Selected compiler -> GnuGcc ->Copy give the new compiler a name
2) Under Toolchain executables tab select your Dosbox as C compiler and Linker
3) Go to other settings tab (you maybe have to hit the > icon to show the tab) -> At the bottom "Advanced options"
4) Here you can define the compiler and linker command line. So it will be generated automatically, so for example in your case:
$compiler -conf DOSBoxLegacy.conf asm $options $file
for the linker the same....
If you could me the exact command line how you have to call the compiler, linker and how the output files are generated i probably could help you better