I have used these resin bonded wheel for the past 25 years professionally and find the better quality ones work well, cheap ones will have problems at times with contamination.
They all need to be "run in" as per the instructions (if all else fails read the instructions). I used a piece of agate with a smooth face and a square or rough straight edge on one side (use the rough edge to knock off the very tops of the peaks only). Use the agate with plenty of water to run the wheel in.
Don't try to smooth the wheel entirely as this will ware the wheel excessively. AVOID PLACING SHARP EDGED OF STONE ONTO THE WHEELS AS THIS WILL STRIP THE RESIN RIGHT OFF.
As to scratches, apart from a contaminated wheel only one thing leads to heavy scratches at the polishing stage. That is failing to check properly between each step that you have completely removed all the scratches from the previous step. Do this by drying the stone and watching the light as it rolls across the surface, if there is a scratch keep working on the current wheel until it is removed, if it still does not come out go back to the previous wheel.
A crack can appear as a scratch as well so check each step thoroughly.
There is no easy way, just practice til you get it right. I hope this helps.