General thoughts
You ask about balance. Balance of what, exactly? Financial power? Military power? Authority? There's no inherent reason that the witches would have access to any of those things. If magic obviates those forces, there are deeper problems with your setup.
Assuming it is a feudal society that interacts with the rest of Westeros, it exists in a pretty sexist system. So the men will be necessary, at least, to interact with outside society. And outside kings will figure out if they are talking to some little chump with no decision making power, so it must be the case that there exists positions of legitimate power for the men.
However, necessary is not always treated as essential, and value is not usually distributed fairly among sexes. How can this setup, where men and women occupy different roles in society because of their sex, be written in a way where everyone is treated equally and valued according to their merit?
The balance of power can be where you put it, depending on how powerful you make the magic (although it seem really unlikely that people will be treated according purely to merit in this medieval society, given that we haven't hit that by modern times -- there will always be a system of patronage/favoritism/politicking). If the separation needs to be so great that the male/female hierarchies are completely non-overlapping, just make sure to show people of similar ranks within their hierarchies. If the High Witch really more highly ranked than the Head Diplomat, on the high council? Hope the spells can prevent an invasion when she over-rules him!
Regarding the lineage
The "sons of society" idea is interesting. I'm not sure what the overall political structure of this House is. But I'm assuming the there's some kind of hierarchy. Presumably, there's some Top Queen and having a person from your clan as the queen confers some perks (depending on where on the spectrum of "absolute monarch" to "first among equals" the position is, it may not be the most important thing, but it still don't hurt to be the boss). Thus, there'd be some political jockeying for the position.
If men are raised as "sons of society" in some clan-agnostic setting (the nature of this neutrality is left to the author and probably will be a good source of a Big Dramatic Moment, sort of like The Watch picking sides), they would probably be trusted to fill in as the neutral bureaucratic layer of the society. A high ranking, ostensibly neutral bureaucratic functionary can be very powerful. See Baelish or Varys.
Another aspect of this could be: are there nobility at all in this house? It could, of course, be a totally flat structure of equals living in egalitarian bliss, but that doesn't fit in with the Westeros vibe at all (and there'd still need to be a high queen of sorts just to be the boss for quick decisions, so this wouldn't negate the previous paragraph). But if there are nobles and peasants, this brings up two thoughts.
First, assuming the noble men are still considered nobles, they still have value. That is, a noble woman will presumably want a noble husband to produce noble children. So, they are at least in as good a position as noble women in conventional feudal society. Not great, but something. Further, because they are "sons of society" the trading for alliances that noble women were subject to historically is not really relevant. As a result, they will have to be judged by some other merits. This would seem to make them more independent -- their value must be somehow linked to something they did, presumably a powerful fighter or brilliant bureaucrat will be seen as a particularly good suitor. Because competence follows interest, it seems likely that they'll have enough flexibility to follow their passions at least. Sidenote -- in this case, the "sons of society" system could be seen as something of a protective union for the dudes. Perhaps they set it up like this to prevent the kind of treatment women are subject to in normal feudal society.
Second, if there are peasants, it is in all the nobility's best interest to draw a line between the two. Noble men wouldn't be, in the very least, relegated to the lowest levels of drudgery. That's what peasants are for. Or golems, depending on the magic.