As an FYI before reading, I've cited a source towards the end of this post for most of the information you'll find in it.
Typically when two dogs are playing rough, it's better to let them figure things out. If your male dog seems to be biting down pretty hard on the female dog's scruff/neck area, and she doesn't seem to mind or still exhibits classic play signs (I'll talk about those below), then you probably shouldn't separate the fight. I also wouldn't physically break up the fight, even if the female dog doesn't like it. When dogs are playing with each other and something out-of-line or undesirable is done, the dogs will let the other know with a preemptive growl or bite (not usually harmful, but just as a warning). So essentially if you have two social dogs who know how to play, they also know how to let the other know to stop playing when something has gone too far.
I talked about indicative behavior above, so I'll cover a few signs of playful and aggressive behavior. Because a lot of dog play looks like it's aggressive and can be misinterpreted by other dogs playing, most social canines have specific signs to signal that their behavior has playful intentions. These signs are forms of "metacommunication," meaning a secondary behavior accompanying the primary action which is essential in interpreting its meaning. In other words, behavior without these metacommunications are ambiguous.
Play bow before and after aggressive-seeming actions. A lot of times, when dogs do something like bite another dog, jump on them, whack them with their paw, lunge in, or something else, they'll do a play bow before or after to signal that there were no aggressive intentions and that the other dogs shouldn't take it as aggression.
Bear hugging. So it's not exactly hugging, but in addition to play bowing, dogs will often bear hug. It looks pretty mean and aggressive, but it's typically 100% friendly behavior and it's a good indicator that your dogs are playing just fine. I'll put in a picture to illustrate how aggressive it looks compared to how aggressive it really is. You'll notice that the dog on the right looks pretty mean -- it's all play.
Trading, sharing, or temporarily stopping roles. A lot of times when dogs are playing, they'll give each other opportunities to trade roles. If one dog is on top of the other, the top dog should eventually give the one on the ground a small escape period where he should be able to stand up and continue playing. If two dogs are chasing each other, the universal "this is just play" metacommunication is for the head dog to slow down and let the other catch up, jump on him, try to get a toy in his mouth, etc... They may, again, switch roles. The faster dog might slow down and let his playmate run ahead for a few seconds.
There are many more, but those are some of the more common ones. Others include wagging bodies (not tails), face biting/teeth locking, and stopping for a few seconds to take a breather.
Above I mention that wagging or having a loose body is a sign of play, but not wagging the tail. Many people think that if a dog is wagging their tail, everything is okay because it's a generally accepted sign of happiness. However, even distressed dogs will wag their tails. When watching dog play, you want to be careful of stiff-bodied dogs, hair standing in a line down the dogs back (raised hackles), and body language, regardless of their tail movements. You can find tons of diagrams that illustrate various body language clues on Google Images just by searching something like "dog body language."
If you're interested in reading more about canid behavior and don't want to read up on those sketchy "how to" links, I highly recommend Canine Behavior: Insights and Answers by Bonnie Beaver which you can buy or view in PDF form here. Beaver has done a lot of great research and a lot of what I've mentioned in my post I've learned from the resources she's written.
In my original comment I also talked about letting out a "yelp." If you're really worried about your male dog's biting of the females neck, you can let out a real high-pitched yelp. This should immediately get both dogs attentions, they'll give you a surprised face, and then should continue playing, but it lets them know that you're not entirely comfortable with what they're doing.
TL;DR: Dogs will know when it gets too rough and typically let each other know. They also have behaviors to qualify aggressive-seeming actions and make sure that if an action that seems aggressive is playful, it's interpreted properly. So don't stop the playing unless you're really worried and see obviously aggressive signs.