Annulment and Child Custody

Hi.. i need your advice.. My friend, married with 2 daughters 9&7 y/o,is not legally separated with his wife(for 5 years now).The kids used to stay with my friend(actually with my friend's parents since my friend is working as seafarer and comes home every after 9 months) until last Sept2011 their mom took them to her place and transferred them to another school. My friend wants to have the custody of the kids. My friend has been religiously sending financial support(allotment) for his kids. Just recently my friend's wife is demanding for an increase of financial support. Their mom is unemployed.. Can my friend file for child custody even if they are not annulled?the kids prefer to stay with their dad,if my friend will take them back from their mom, is their any grounds wife can file against him?if there is,then what would it be? Thank you so much..

i recommend he files a complaint for custody, but once i have doubts it will prosper if he will just leave them with his parents. custody can't be exercised through proxy.

Thank you so much Atty for the reply..
My friend got a weird idea of taking the kids and when their mom will come to pick them up, he will tell his wife to file for child custody first.. he desperately wants to have his kids with him. His wife has filed cases against him one in her province and another in POEA.
My friend wanted to make sure that the money he's sending for his kids will not be spent for something else. He is thinking that (maybe) his wife is spending the money to file cases against him.
Will his "weird" idea work? If he will pursue with his idea, what will be the consequences?
Thank You so much Attorney..

if he's willing to stay here then it can work, but I recommend he be the one to file the case for custody.

thank u attorney for your time..
one more thing attorney, my friend also, has a 1 year old kid with another woman. His wife doesn't know about it yet. How would that be Atty? What should be the best thing to do first? sorry,his lovelife/married life is a bit complicated.

if that is brought out, it will weaken his chances because he has been involved in immoral acts, but it will not automatically disqualify him