You are asking for a solution to the headache of the century (as there is no good or perfect translater site, all have their faults unfortunately ), in my opinion, one solution can be, you translate on different sites and compare the results then try to find the right (or the the closest to the right) answer (translation), another solution, find your own translator or translators (reach some agreement with someone or some people to translate for you, you can pay them or something , of course providing you don't want or know how to translate).
If you're looking for a good machine translation, there's really none that can do a perfect job. If you want to translate it, I would recommend learning some of the language, using a dictionary for words you don't know, and looking up grammar points you don't know. I would recommend jisho.org as an online dictionary. Rikaikun, a Chrome extension is also pretty good and allows you to hover over words on a page to look them up.
You can learn the language a bit, then you can directly read the raw with rikaikun and furigana add on as assistance. it will be hard at first, but after a while, your vocab will increase and you will have it easy in the end.
Best advice I can offer is to use both Google Translate and Bing Translate. Reading them both should give you a rough idea of what the chapter is talking about. Then, if you want better details on specific sentences that are still jumbled up, you should try throwing them at jisho.org, it's an online dictionary that can give you a pretty accurate definition of things word by word, so you can try piecing it all together when remembering the context that google and bing gave you. And I honestly suggest never touching systrans again, of all sites I tried, it was by far the worst. At least for Japanese novels.