I am in the exact same situation. Travelling with spouse, a 4 year old, and a 2 year old. Ticketed through United with codeshares.
VIE-FRA-DEN (LH) DEN-HLN (UA) outbound and HLN-DEN-ORD (UA) ORD-VIE (OS) return.
We do this trip every year and up until now, have been able to call in for seats.
Just got off phone with LH- they say I have to wait until 24 hours ahead of time for check in to get seats.
Hopefully at least the 4 year old and 2 year old get seated next to each other.

Next trip will likely be with United miles, so maybe this won't happen?