The GTR is a plugin that modify the signal in real time.. It is totally normal that on your track if you remove the plugin, you'd be left with the clean signal.
I don't know aboute acid, but most recording software have a freeze fonction, which will process the audio with the effect and deactivate it while leaving the processed audio on the track.. this might be what you want. Or, when exporting the song it should process all the effects inserted on the tracks..

The only exception to this is if you use GTR as a stand alone app, the signal isn't processed within Acid so you will record only the clean signal, unless you choose the GTR as an input in Acid instead of the actual physical input... Hope this make sens ! ;)

i need to figure out how to open/conect waves audio GTR guitar affects software to/with acid music .

how do i choose the GTR as an imput ?

Not sure specifically for Acid, but most daws have a "mixer window", and little spaces/slots that you click on called "channel inserts". You should be able to click on the insert, and a list of the effects you have on the computer will pop up. Select GTR and it will load.

Then make sure your record enabled, and you've selected watever input your guitar is plugged into, as the input for the track.

You should see the meters on the mixer channel moving, and hear the GTR pluggin sounds.

A bit old but it might help :

hi, ok,
why is it that i cant hear the guitar i am playing untill its recorded , i finally got things working where i am able to record my guitar and effects using my guitar pedal and not have to use plug ins and software issues , but now the only problem i am having is that i cant hear my playing and the effect untill after i finish recording , ?? why cant i just record something and here what i am playing with efferct rather than just here my strings ,

ps, i have searched all of you tube and there is nothing on this .