SOmething came up yesterday we were not sure how to resolve - it was our first use of the tides of battle cards.

one house attacked another - both had 1 unit each, The attacker won, and had a sword on his card, but the looser drew the tide of battle card with a +0/ skull on it - also eliminating the attackers unit. This happened twice - we allowed the attacker to take the region, as long as they could place a power token in it - but is this correct?

You place power tokens only when you leave land area voluntary. In your case, the area would simply be left empty after battle. Also, if defender had a power token on that area, it should be removed since defender have lost control over the area.

Ah - so area in effect becomes a neutral teritory and has to be captured again?

that is correct. yes