On any diffrent input layout use android:keyBackground=".."
example:
input.xml:
<com.example.KeyboardView
        xmlns:android="http://schemas.android.com/apk/res/android"
        android:id="@+id/keyboard"
        android:layout_alignParentBottom="true"
        android:layout_width="match_parent"
        android:layout_height="wrap_content"
        android:keyBackground="@drawable/blue_key"
        />
input1.xml:
<com.example.KeyboardView
            xmlns:android="http://schemas.android.com/apk/res/android"
            android:id="@+id/keyboard"
            android:layout_alignParentBottom="true"
            android:layout_width="match_parent"
            android:layout_height="wrap_content"
            android:keyBackground="@drawable/red_key"
            />
then on OnCreateInputView method:
@Override public View onCreateInputView() {
    if(theme == 1)
        mInputView = (KeyboardView) getLayoutInflater().inflate(R.xml.input , null);
    else
        mInputView = (KeyboardView) getLayoutInflater().inflate(R.xml.input1 , null);
    mInputView.setOnKeyboardActionListener( this);
    mInputView.setKeyboard(mQwertyKeyboard);
    mComposing.setLength(0);
    return mInputView;
}
and on the end of the method onStartInput add this:
setInputView(onCreateInputView());
If you've already done it and what you need is to set a different background to special keys. Maybe the solution to my problem that I wrote will help you: https://stackoverflow.com/a/18354298/2683898
Good Luck! :)