It's just a matter of time on the water, your legs will get use to it. Also, you'll start to learn the different currents that different harbors can produce. Based on that you can make educated decisions. Huntington Harbor can be the worst for currents.
Most importantly, don't fight the currents, use them to our advantage. If you see that your trip is going to start on an outgoing tide all you have to do is change your launch point to be further inside the harbor. That way you just let the tide push you out and since you launched further inside that means it won't push you all the way out. Then wait for the tides to change and it'll push you back to where you started. If you're starting at an incoming tide just reverse the steps and park at the mouth of the harbor and let it push you in.