when to use c.lk : whenever you think they'll try to jump.
when to use grabs : whenever you think they won't.
More seriously :
If you are against an opponent who always jumps during resets, you have no reason to use any grab (except excellebella, but it's situational). If he tends to jump, do c.lk into combo. You don't need to change that until he adapts and start blocking low. And that's where you can start to grab.
The reason why you saw grabs after grabs in some sets is that the opponent was simply thinking "there's no way he going for a grab again, he will c.lk this time". That's simply a matter of mind games. There's also the fear factor : sometimes, they don't know if you'll grab or go low, but if they guess wrong, they'd largely prefer to eat the damage from a grab starter than from a c.lk starter.
In neutral, that's a bit the same thing in some situations. You jump in, they block, you have the same choice than during a reset, go low or throw. It is important to vary between these solutions when you get in with a particular move, else they'll adapt and just do the same thing to avoid your choice every time.
But that still wasn't real neutral. In neutral, your main grab is MGR. MGR is there to force people to jump, because they know if they don't they get into the danger zone and risk dying from it. You don't need MGR to connect for it to actually be useful, just having that possibility gives you an edge. If they are forced to jump most of the time, you know they'll be in the air most of the time (duh), which narrows down the number of possible situations you will have to face. Knowing that they'll be in the air means you can go for preemptive counter measures, like using j.mp/j/hp, excellebella, air throw, s.mp.
Not having the occasion to grab isn't a problem. It only means your opponent gave up a lot of his possibilities just to avoid one of yours.
And even if they jump all the time, you still have ways to connect a grab! The best example of that is punishing badly spaced whiffed jump-ins. As the opponent can't guard or jump or act in any way for 2 frames if he lands while performing an air move, you can mgr an opponent when he's falling and you see he's too far to hit you. He lands, mgr connects, you win. Also works for whiffed cross ups with diamond drop.
Now that you showed your opponent that being all the time in the air isn't the best solution. So sometimes he stays grounded. Awesome! Now you need to identify when he does stay grounded. That the moment you get in and instead of going for the anti-air counter measure, you warmly thanks your opponent by grabbing him!
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That's a bit simplistic, but it's generally true. The hard part is applying this, and the only way to do it is to analyze your play and your opponent's in real time. Experience and post-match analysis will immensely help. Look for situations that force your opponent to be on the ground, see if it is possible to get in range for that occasion, and ALWAYS try being unpredictable.
PS : don't say "pro skullgirls players". They don't exist. for now?
I know you just meant "good", but it's something that makes me laugh every time I read it :^)