just have a look @ your waveforms .
the room mic starts later in comparison to your close mic .
nudge the room mic so it starts at the same point where the close mic starts .
( not the region , the waveform ! ) .
now zoom in and take a look again if both waveforms do the same " movement " . if one f.ex goes up and the other goes down , flip the phase on one of them .
make sure you have f.ex the trim tool on both tracks ( just sounds kinda different to my ears , if its just on one ? maybe it depends on the pt version ? )
now you have alligned the close mic and the room mic in phase .
if you want more room sound you can easily throw a short delay on the aligned room mic as well .
its better to record it right , but the method i am describing can most times FIX the problem , depending on what you are looking for ?
a cool idea for finding the right mic position , our beloved ecue mentioned , is to play a sine wave through the amp , set up your close mic , flip the phase on the next mic and try to find the place where it has the " most cancelation " , after that you flip the phase and this should be a cool starting point . ( well of course a sine wave isnt a guitar , but if your on your own , and ur running around in a rec room , wearing cans , and playing guitar with one hand and holding the micstand in the other , it gets kinda complicated )
good luck