You have to do the initial alignment with the HC, then you can use SkySafari thereafter. I would resync if you moved a few degrees off target, but to be honest, it's so easy to do, I follow this sequence:
1. 1-star alignment using HC.
2. Connect SS, slew to 1st object (it should be in your widefield eyepiece FOV)
3. Centre object, and do local sync in SS
4. Slew to next object (when ready) - it should be close to centre of FOV
5. If you like, centre to get the optimal view, and sync again
6. Repeat 4-6 throughout night.
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