GTL's should only need to be "thought of" for a period of time, then you can focus your thoughts elsewhere. For most standards, there are only actually a few GTL's (just speaking of the typical 3/7 GTL) that once you internalize you'll have the essence of the progressions in you ears. All 2-5-1 progressions have the same GTL, different notes sure, but the same pattern of descending half step motion. A GTL by itself won't help you make 100% coherent lines because you still need to consider the tune's melody, contour, phrasing, etc. GTL's are, to me, target notes but remember the other chord tones besides the 3's and the 7's. They are probably the strogest, but not the only ones.
I try to take melodic cells from the melody and, in practice, do some permutations in phrasing, note values, melodic contour, etc. and build my lines from the melody as much as I can. To me, how else can someone tell if I'm playing How High the Moon or Ornithology if they didn't hear the melody.... "Good evening folks, now we'll play Rhythm changes in D..." HUH!?
I'm with Kelly and Neff where I pick landmarks where I want to take my line and focus on strong resolutions at those points, and then try to actually stick somewhere near my plan..
I do my best not to noodle around aimlessly.