So i'm using Reaper and working on an acoustic track and I wanted to apply some effects to both the guitar tracks. So I made a new track and bussed both the guitar tracks to this one and applied the effects. It added the effects but it also made itself a third guitar track.. So now I have three guitar tracks but I only want two.. Is there any way I can fix this?
Paul Reed Smith SE Custom
Paul Reed Smith Mike Mushok Baritone
Squire Bullet
Carlos Acoustic
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Mesa Boogie DC-5
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You could just make a group buss for the two guitar tracks and load up the effect on the group buss.

If you've got your effects at 100% wet, the way you did it should work to where you've got your two original guitar tracks then your buss only has the effect playing so you can then mix it in with the originals.
Let's party.
if you mean that you have three things playing now, you need to change the two tracks being sent so that they dont output to the master.

if you are using something like reverb, do like Adam said and set it to 100% wet. then you use the volume fader to set the appropriate level in relation to the dry tracks.
Create an aux track (post fader). Put reverb set 100% wet on the aux track and keep the fader all the way up at 0. Send however much of each guitar track to the aux track. Instead of changing the volume of the aux track, you just adjust the sends that are going to it. This way you can send as many channels as you want to one single verb and still control the amount of verb on each individual track by their sends.

This is generally considered the "correct" way. Of course you can work however you want and whatever gets the job done is correct, but especially in the analogue days, this is the easiest and most efficient way to use effects. It's also why a lot of mixers have dedicated "effects return" channels.
I've been wondering this myself actually. Started using bus channels for effects.

Having the effect at 100% should I turn the dry level right down? Or will that cut the signal completely?