hi, I use WinArm and custom makefile.
to use custom makefile goto menu Project->Properties
tick the box that says "This is a custom makefile".
Set your toolchain.
goto menu Settings->Compiler&Debugger
on the selected compiler you might want select
the GNU ARM GCC compiler and click the copy button
then rename it to whatever you like.
On the toolchain tab change your compiler's installed
directory to wherever yagarto is installed.
I actually just installed yagarto to verify this,
but i got mine installed in C:\yagarto btw. (Yagarto installer
prompted me to install in it c:\program files\yagarto).
Then you could verify if the executives are actually pointing
to yagarto install dir when you click on the ellipses beside the
*.exe's. You might also want to add something on the "additonal
path" tabs.
I almost forgot, you might want to rename your target (e.g build,release)
to whatever you use if you call make manually (e.g. make all).
Another way would be to goto menu Projects->Build options...
goto the rightmost tab with label "Make Commands", it's
prob'ly hidden click on arrow, and change $target to "all" for example.
I think that's it, 'hope this helps.