i hear you. i actually just learned recently that katakana is sometimes used to show emphasis as well though, ever since i read that i'm suddenly noticing it being used that way a lot, i just never realized it i guess. i think it may have even been that app where i read it not sure.
anyway like i said you can flip back and forth in kotoba between the lessons and the dictionary so you can look words up quicker that way than fumbling with a seperate dictionary, i find it really helpful. cause yeah like you said sometimes the readings they show isn't the most commonly used, and i have a hard time telling which reading is which etc etc and for now i prefer to just learn the most common words. once i have those down i can go browse through and learn some of the other readings
i always write whatever i'm studying. when i do lessons on livemocha or watch irasshai or anything, i write out everything. i find it's really helped with my hiragana a TON. before i started doing that i was still getting some kana mixed up and couldn't always remember certain ones. now i still sometimes have to look at it for a second, it's not instant like reading english, but i have no real difficulty reading hiragana. i'm hoping this method will help with katakana and kanji as well so i'm gonna keep at it. going through lots of paper but oh well. technology is great, i love that i can do all this stuff online, but sometimes nothing beats a paper and pen especially for retention.
i just did a couple of lessons in LM (I see that Hava's on too, i'm catching up to her lol except that i don't do all the submissions so it looks like i've only half completed 101 and she has a shiny green 100% but in terms of lessons i think i'm not far behind her)
and i'm starting to have long blinks (lol not quite falling asleep but my eyes don't want to focus) and i'm in a university library so falling asleep would be sorta embarassing hahaha. so i think i'll do a bit of katakana writing practice and then watch some drama lol