I have 2 separate shipping profiles in my shop.
Profile 1: For stickers, has the option to choose free shipping (USPS stamp) or pay calculated shipping (roughly $3 for tracking)
Profile 2: General shipping calculated based on item weight. Used for all other items in my shop.
When customers order a item in each shipping profile it adds the shipping together thus charging them double.
Is it possible to have it so stickers are free or tracked and if they order another item say a shirt it uses the total package weight and doesn't double charge them?
At this time, without an app there is no way to disable combined rates natively if you have multiple shipping profiles. Many people are facing the same problem as you and I recommend you raise the 'stickers profile' price a little and offer free shipping only. So you don't have to worry about double-charge shipping fees when Shopify combined rates at check out.
You can also find some third-party app that works on your case as well.
Hopefully, it addresses your problem somehow.