If you want to specify which polygons get joined to which other polygons you can add a field with a simple numeric code. Give each polygon the code of the "new polygon" you want it to belong to and then use this field when you run the "dissolve" tool.
I'm not sure I understand what the data you are dealing with are like. How are you hoping to decide which polygons get merged together? Could you perhaps post a screenshot of what the data look like?Thanks!
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