My first questions are:

Can a serious D/s relation exist solely sometimes (i love my wife very much and i like her non-submissive a lot - i don't want to loose that)?
My husband and I are trying to sort this out as well. To answer your question above, yes, it can exist as a sometime thing. You might want to communicate thoroughly just when that "sometime" is and isn't to be.

And what steps should be made in order to assure a proper separation between both states? Steps for me and for her.
Seems to me you two will have to decide that for yourselves. Do you want her to kneel at your feet to let you know she's ready for that kind of time with you? Does she want you to grab a handful of her hair and push her to her knees to let her know you want some D/s time together? Are you going to limit those activities to certain times of the day or week? However it begins, you probably would both want to make sure to have time to transition time afterward. Not much worse than having to go from total D/s to vanilla in no seconds flat. Screws with a mind, let me tell you.

Here's a thread where some information on just this topic is covered.

http://www.bdsmlibrary.com/forums/showthread.php?t=8618

(You can thank Tom of Sweden for teaching me how to put this link in the post. At least I think he taught me. We'll find out as soon as I submit this. As part of his lesson was an image entitled "duh", I've somehow gotten the idea that doing this is supposed be a simple thing. Imagine that. Despite the basics, sometimes I can turn the simple into the screwed up without even trying, so we shall see.)

I hope this helps you. Good luck with your new venture!

tessa