When you actually consider the Atom's powers he's one of the most dangerous beings in comics (really underutilized though). That said I agree that the Atom will have to be a little more creative than just stomping his brain. I do believe that a clever plan of attack (should the Atom manage to enter the Juggernaut's body) on Atom's part could drop the Juggernaut.
Juggernaut 8/10
__________________
“Where the longleaf pines are whispering
to him who loved them so.
Where the faint murmurs now dwindling
echo o’er tide and shore."
-A Grave Epitaph in Santa Rosa County, Florida; I wish I could remember the man's name.
There is really nothing Juggs can do to harm or find the Atom. So by default it's an 0 - 0 draw, if you think that the Atom can't hurt Juggs. Otherwise Juggs 0 Atom 2
How would you know that?....Nobody realy knows what is Juggernaut capable of, because he himself dont' use ALL of his enchantemts properly, other Juggernauts have cooler showings because they KNOW how to use them, but I'm not saying he will never do....
I hope one day he learns how to use his powers fully.....can you imagine that...!!
Consider this, Atom and Hank Pym/Ant Man's powers are basically identical, except Ant Man can grow as well. Recently, Ant Man got inside Luke Cage's body, who is billed as having unbreakable skin. Although he's obviously far less durable than Juggs.
Ant Man tried to grow inside Luke's body, and he couldn't do it, since Luke is just as tough inside as out. If he tried to grow, he himself would have died in the attempt, and Luke would've been just fine.
Now imagine if Atom tried to grow inside Juggs, instant death for him, and Cytorrak probably ports him out of Juggs body because he'd become an inconvenience. Nothing has really hurt Juggs besides TP, and Nimrod's neural/sonic beam, Atom has nothing to bring to the table.