If she's stayed on her own quite happily, and has not been clingy when you leave, then I would suspect that she won't mind that it's both you and dd1 leaving her in the morning.The fact that she's staying for the full morning won't matter either. 'Settling in' means that a child has understood that mummy/daddy/carer has dropped them off at nursery but will be coming back. A two year old usually follows a fairly standard pattern. First visit with parent, child may be initially shy but then discovers a whole room full of toys/other children to play with and is reassured by mum/dad sitting in the room, mum/dad usually then has to drag an indignant child home! Second session parent leaves child, child cries and is given one to one care by a 'key worker', this usually involves the child being carried around for the whole session by the staff member so that they know that there is an adult who is 'theirs' for the session. Parent picks child up after a couple of hours (after 'phoning or being 'phoned for reassurance during the morning) Second day, child may be upset at drop-off time as they know parent is going but 'key worker' should be on duty to provide one to one again, child will spend less time being carried etc and will start to join in or play with toys. This carries on and usually, (though each child is different of course,) takes about four sessions without parent. Child eventually skips into nursery with barely a backwards glance, secure in the knowledge that they have all day (or half day) to play and that parent will come back to get them.
Sorry this is so long-winded. If your child is happy to go into the nursery and is not upset when you leave, then I wouldn't say anything at all, if she's happy she'll probably enjoy the fact that she has her own special place to go to, that dd1 can't, and she won't be remotely bothered that ds1 is leaving too.
If she is still upset when you leave then a white lie is in order and you'll need to tell her that you're taking dd1 to school too. She'll be upset when you leave, whether dd1 is there or not. The issue of leaving her for the whole session won't make much difference to her either, 2 year olds are not really aware of the passage of time and, in any case, a two year old's day is marked by events. The staff will tell her that mummy is coming 'after lunch' or 'after we've had our story'
Good luck! She'll be fine and will probably say 'Mummy? Who?" ten minutes after you've gone and she's discovered the sand tray.
Hope that helps.