It can be especially hard on days when your schedule overlaps, but living in the same house will make it a little easier. The part I missed the most was sleeping together (less cuddle time). Other than that, we did pretty well.
When we had opposite schedules, I was working from ~9am to 5pm and my boyfriend was working from 7pm to 3am or from 10pm to 6am (various schedules, he worked a couple of different jobs where he was on graveyard). We only had one car, so he would take it or I would drop him off and pick him up. We would spend the time in the car talking. I would make breakfast for him when he got home in the morning before I went to work and he would make dinner for me when I got home before he went to work. Mine was a Monday to Friday job while he worked various days. On days when we were both off we'd make the most of it. Sometimes we were really tired, but I think it was worth it. Ironically, I think we actually spent less time together when he got a 9-5 Monday to Friday job because I was home alone awake when he was working loads of overtime.
All of that to say it can be done. I think actually your time together gets better because it's less available - quality because you don't have the quantity. Come up with some plans together. Make sure you schedule some things to do together when you're both off at the same time. Also make sure you each get some time with your friends (could be accomplished while the other is at work I guess).
Also, if this makes the financial situation in the house better, it tends to make everything better because it eases a lot of tension.