To merge different sets of listings into single entries for each channel:
1) Download, install, and open Guide Tool
2) Click on Merge Tuners
3) Adjust the priorities as desired so that ATSC/clear QAM tuners show up first
4) Select Channel Call-sign
5) Click OK
This can also be done manually for individual channels by going into Tasks > Settings > TV > Guide > Edit Channels > channel > Edit Listings, selecting the appropriate listing, and choosing the merge option.