the longer 'Ciebie' for sure at the beginning and the shorter 'Cię' at the end. Otherwise you will be understood with no problem but it'd just sound a bit unnaturally for natives :) for the place in the middle of the sentence I'd say that both are okay though we use shorter forms even more often as a quicker alternative.
I would say the matter of ę is purely ortographical :) you can also write 'Ona cię kocha' and it's also correct. The thing with personal pronouns is that we do have them in longer (i.e. ciebie) and shorter (cię) versions and thus generally we use the longer ones at the beginning of sentence and the shorter at the very end while in the middle they usually can be used interchangeably (though shorter are used more often, I believe). Still, that's just general rule - the more you know, the more you feel it :)
It's mostly after, however it rather shouldn't be at the end of the sentence, if it can be avoided.
"Ona kocha ciebie" would be like "She loves YOU!" (and not him).
Actually, using "ciebie" even with this word order is already emphatic (but more like "She LOVES you"), for a neutral sentence you'd use "Ona cię kocha".)
I'd say that rather simply "she loves you". If you were to say the first, you could say "Ona kocha tylko ciebie" - "tylko" means "only" so you'd say then that "she loves only you (and not anyone else)".
Of course in speaking this simple sentence we're talking about can be of the first meaning, depending on the stress given. But after all, there's nothing strong about the words themself :)
it's called declension. have a look at pronouns https://pl.wiktionary.org/wiki/Aneks:Język_polski_-_zaimki