From Baseline to Proposed model, or from Proposed to Baseline?

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Reasons to start with Baseline model:

1. If you are modeling for a program that takes credit for beyond-code buildings and the program requires you to document the impact of each measure individually, it is often easier to start with the baseline and add each measure stepwise, documenting the savings at each step. This is a common requirement of utility design assistance programs.
2. If you get involved with the design process before major design decisions are made, you can model individual design choices as they are being considered, and hopefully help guide the decisions. Having a neutral baseline can help the design team avoid biases involved with picking one of their designs as the baseline and judging everything compared to that.

Reasons to start with Proposed model:

1. If the plans are already done and you can't have any impact on the design, start with the Proposed and hopefully you can use one of the things @Amir Roth mentioned in his answer to automatically generate the Baseline model from the Proposed model. IMO, this is misses the point of energy modeling as a design tool, but it happens all the time for LEED.