i have what might be considered a slightly complicated setup for a variety of rokus
roku.com account #1: N1000 has its own account since it can only hold a few  channels and it runs my netflix, amazon VOD and my hulu plus account
roku.com account #2: roku XD/s #1, my friend's roku XD/s #2 at HER HOUSE, my roku2 xs.
-- XD/s #1 and roku2 xs are on my netflix, amazon VOD and my hulu plus. XD/s #2 is on her netflix and amazon VOD [and my hulu plus, oops!] but it's on MY roku.com account because she bought her XD/s post youtube removal and that was the only way we could get youtube on her roku.
and yeah, it's set up with a PIN for paid channels so she can't charge stuff to me.
when my soon to be roommate moves in this january she's going to put her netflix account on the N1000 but the rest of it will remain on my account.
if you could follow that convoluted mess you can see that the channel linking is completely unrelated to the roku.com account for channels that you pay for outside of the roku accounting system. but if i bought a roku game with my remote on my roku, i'd have to pay for it again to get it on the second account.
N1000, roku1 XD/s, roku2 xs, roku3