Is there a way to allocate mortgage interest and taxes between schedule e and schedule a? Or do you have to do it manually.

[sjrcpa]

If it's a vacation rental, the software should do it for you after you enter rental and personal days.

If it's because it was a personal residence  for part of the year and rental property for part of the year, do it manually.

[George4Tacks]

The 8T tracing rules would have to be done manually. 

https://www.law.cornell.edu/cfr/text/26/1.163-8T