From my experience of using ATLAS, the trick is to look for key words. Mecab and Jparser are very helpful in this regard when ATLAS gives you bad translations.
If you've watched enough anime, you'll probably have some sorta of amateur level of listening to Japanese (hopefully). Listen to the dialogue to get a feel of the context, find key words, then mix things around with the rest of the ATLAS translation to get the gist of what's going on. That's how I get things done.
Shin Koihime Musou is definitely the type of game I wouldn't recommend to a first time ATLAS user because it goes beyond simple mouse clicking. If you're actually interested in ATLAS, you should try some ATLAS friendly games to get the hang of using it.