I think he might have first been with her because she was convenient.
It upset Michael, who he hated.
She had a home, which he needed since his divorce and losing his other house and his money.
She looked after him, which he enjoyed.
It upset Anna to have him on the Street, and he hated her too.
It gave him somewhere to live and be looked after, and also the opportunity to needle at people just for the fun of it.
But I think he did come to love her. When he thought she was in danger from one of Vinnie's thugs he went running down the Street looking for her, he was properly upset at the thought of her coming to harm, and properly relieved when she was okay.
And then he found Nicola and had the chance to be part of a family, and he really wanted that.
Plus he had a passport for Eileen when he went on the run. He wanted her with him.
I think as much as Phelan could love anybody, he loved Eileen and Nicola.
In his mind they have betrayed him though and so now it's all about the baby. I'm not sure he'd want to kill either of them, even now, but I think he would hurt them to get the baby if he had to.
After all, he could have killed Gary and Sarah but he didn't. If he can spare those two when he hates Gary and thinks nothing of Sarah, he'll spare his family if he can.