you are getting your notes and modes confused. a note is either flat or sharp, a mode is minor or major to a relative key. its a common mistake.
Am is a flat 3rd 5th and 7th to the tonai or root key, so in this example it would be the key of C major.
the only one you have to watch out for is anything going from a C to a B would be a whole step note wise but only shifts half a step in the fretboard (ie a B# is a C, not a Cb) now whether you are relative minor or major from that particular key just make the 3rd 5th and 7th notes of the major of that root note and you are now in relative minor....if of course aeolean (sp?) is the minor mode you are trying to go for which depends on the song.
alot of times when i did cover songs in different keys starting out, i almost always had a guitar in front of me and went through the song in chunks - chorus, verses, interludes, intro's, etc. to find the keys. normally it is not that hard, since a song will repeat most of it all the way through at least once or twice. if you are comfortable with theory then you can do it all in your head but it can get confusing if you do not know how the fretboard works - so dont try to make it harder than it really is - use whichever method you need
PS. it might also help you to go read the "explain modes to me" post in the music theory and technique section of the forum - alot of information that pertains to this post will apply here to what you are trying to do and possibly make it alot easier.
