I used to just ignore linking footnotes because it was so much work, but now it works great. Create anchors, then when you want to link, you just click on link button and a list of the existing footnotes comes up. This list keeps you from making mistakes, because if it isn't there you messed up somehow.
One thing it does not do is check to see if you start the id with a number which is not permitted. I understand though, that this check will be in the next update.