Hi @Melanie15 - Glad to hear the basals are getting better.
I am still doing shots (but have ordered a pump)… With shots I give the carb bolus before the meal (usually 15-20 minutes before or later if it is really low GI) and then do a follow up protien bolus about 45 minutes to 1 hour later (I watch my CGM to time this). Taking two shots is inconvenient for me so that drove me to trying a pump.
For the pump - your description seems right, you add the carb carbs and the equivalent protein carbs and deliver the protein portion of the carbs as the square wave. My understanding is you can also watch your CGM and cancel the square wave if you start to drop too much. I will find out more about this when my pump arrives 
Here is a link to an old spreadsheet from @Terry4 that helps explain how he did it in the past (if you are a spreadsheet person). I think he is now using a DIY closed loop pump that automatically adjusts his basal so he has changed things up and just relies on the Loop to adjust his basals for protien. I personally can’t wait for a commercially available pump to come out that automatically adjusts basals.