you can add proguard-project.txt to your project inside it you must set options you want form progoard for example i write these options
-optimizationpasses 5 -dontusemixedcaseclassnames -dontskipnonpubliclibraryclasses -dontpreverify -verbose -dontoptimize -optimizations !code/simplification/arithetic,!field/,!class/merging/
to check you can export your app to apk
an then you can use dx2jar to found if it is protected or not