I think you mean the same question as in http://www.italki.com/groups/1067/topic/33691.htm
Generally speaking, the goal of every translation is to express the original text in the way the author would have written it in the target language, if he would have known that language. You're a native speaker of Hebrew, so you know how one would write it in Hebrew. So just write it this way :-)
The problem with the CAPS-LOCK key you mention seems to be related to your software. If you switch writing modes, the software shouldn't scramble the rest of the text. So either your software provides another way to switch modes, or the software is stupid. In the latter case, use a different software.
I don't know how Israel people mix roman letters and hebrew letters, and again, you're in a better position to know that than I am. But if I was writing a German or English text, and had to quote words in Hebrew or Arabic, I would keep the original writing order. So the main text is left-to-right, any short quote is embedded and right-to-left, and any longer quote gets its own paragraph to avoid major headaches for the reader (or the writer). I'm not sure if that is what you were asking, though.