for pad's i just add pad in the schematic, with a library of pad parts. i don't know if theres a better way.
the off grid junction thing i came across a couple of days ago myself when i edited someone elses schematic, it wouldn't place a junction or connect the wires since the grids were off. So this is just a matter of standardisng the grid before anything is created, the default grid i find is too coarse.
you can write a script that will realign the packages to the grid, which is useful for this sort of thing, there's probably something already on their ftp site too.
i did find eagle fairly intuitive to pick up, but then i like the scripting and command line aspect of it, so i think its just what you're used too. we use protel99 at work and i did find it a steeper learning curve.
Didn't really find the ui that bad, if i'm making a quick circuit i'll usually do it in eagle, you just have to learn its odd quirks, which i think they all have in some form. i think if you're used to the bigger pcb packages you'll struggle with eagle, but for the first timers it seems easier to pick up, but then you'll hit its growing curve , which is why i always recommend A!tium to newbs, but they'll balk at the cost and go with eagle, epecially since most open source hardware stuff seems to use it too.
A!tium just feels like the 600lb corporate gorilla and not as friendy an enviroment to get into, eagle gives the impression of beign a bit more 'hacker' friendly. It's that mob mentality, you see other people using it, so you do too. I'm sure A!tium aren't strapped for customers, but I reckon it couldn't hurt them to look at this enviroment like Ti tried to do with the MSP430, but only if they can give that same feel.
its also good to use the vector font option, sparkfun have a nice introduction to setting up eagle for the first time.