The Senior Staff just answered a similar questions
here, so you might want to check that one out too.
Basically, you'll apply for the song at either network - the one at TFL will be for the actual, full single and should reflect such; the one at AFL will be for the anime opening/ending theme only, and should reflect that too. Applying at one network and getting approved, does not necessarily guarantee an approval at the other. If you're applying at the same time, it might be wise to say you are applying at both networks in the comments, but again, it guarantees nothing.
If approved at both networks, you're correct in that you just need to link both networks to be okay. :flower: The layout can feature either the TFL version or the AFL version, though I believe the codes should reflect both. I think this is what you're asking, right? :unsure: