I havent used tone scholar but ive used apps to augment regular practice.  I used them when i couldnt get my instrument and play.  Not so much on violin but alot when learning guitar fretboard layout.

for ear training..

checkout fiddlehed on youtube.. specifically for CALL AND RESPONSE type training.  Its an excellent way to practice new tunes.   Its a method of repeating back small musical phrases... or playing parts of a tune while someone else plays the other.   you can use that method with a recording.   like play an mp3 of some tune but only concentrate on a phrase at a time.  once you have that phrase ..swap to another phrase and only play that.  then piece it all together.  He on fiddlehed can explain it better.

Listening to the music you intend on playing is one of the biggest helps.  listen till you can hum or sing it.  I assume we arent talking about ear training for classical type music.

which brings up the fancy fiddle shows... sometimes it takes listening to those.

As far as recognizing individual notes ..like someone plays an F# and you know its an F#.. things like that work themselves out by either practicing scales a bunch or playing tunes a bunch.  It starts to become easier and youll just know where the intervals are in a melody with time.  So a mixture of scales, tunes, and arpeggios would be a good routine.   warmup with scales.  play or practice a tune..work in arpeggios after a bit.

When you practice arpeggios youre practicing broken chords.

others will provide links im sure.  theres alot on just this forum.  i cant remember where it all is.

hope that helps some...it just takes time.  

@invisiblewasp maybe videos along these lines help some