accept in advance that you will take the short end of the stick. what i mean to say is that although you want to see them every night, maybe dad will want to take them to the pool to which you graciously say have fun! its hard hard to be the one at home and its even harder trying to herd cats to be on the computer at x time (I've been on both sides of it). we've found that lots of photos and texts work great. also there was almost always an aftermath of skype. the kids miss you, the person who is home bears the brunt of it.
consider reading up on tips for reintegrating with spouses (they have classes about this for people who travel a lot to hard posts because it is hard to be the person that was away and its hard to be the one that stays behind)
sticker charts with the numbers of days left have worked to help my LO mark the time.
do as much as you can before you leave to help the other parent whether thats freezer meals or planning breaks by setting up babysitters etc.

OP - wanted to chime with a take from someone who has been on the other side. When I was a child, from 2-5, I would not see either of my parents for six months a year (they worked somewhere where they thought it was too cold to keep a small child). Every early fall, they'd send me to my grandparents and every spring, they'd pick me up. That was before the days of Skype.

I am not scarred and am very close to both my parents. In fact, I barely remember the separations. Your kids will be fine and you are certainly entitled to doing a job you seem to both like and need.

I've never had to go away for three months myself, but when I do have to go away for a few days, I make sure to facetime every day; you can also record a book in your voice to be read at bedtime.