Hi Dimitrios,
The first question is which of the two languages is the most important to you? That is the one you should prioritize and give the other language the subfolder. The next question is are the English pages intended for the same country, but in a different language? if this is the case, then you should also add the hreflang attribute so that Google knows which pages should be served to what type of users.
If you have follow up questions about hreflang application, here are a few resources for you:
http://moz.com/blog/hreflang-behaviour-insights
http://moz.com/blog/using-the-correct-hreflang-tag-a-new-generator-tool