How to prevent second OS X partition from seeing apps in the other partition?
Unmounting the 'unwanted' partition before installing the new application should help in most cases:


Quit all open applications
Start Terminal.app and enter diskutil list


output looks like this:  

 #: TYPE NAME SIZE IDENTIFIER
 0: GUID_partition_scheme *121.3 GB disk0
 1: EFI 209.7 MB disk0s1
 2: Apple_HFS Yosemite 60.2 GB disk0s2
 3: Apple_HFS Mavericks 60.3 GB disk0s3
 4: Apple_Boot Recovery HD 650.0 MB disk0s4  



determine the identifier of the partition to unmount by size/volume name and enter diskutil unmount /dev/IDENTIFIER
(in the above case diskutil unmount /dev/disk0s2 to unmount the 'Yosemite' partition)
To remount this partition afterwards just enter diskutil mount /dev/disk0s2