Yes, Shrimpy supports the ability to segment your funds into multiple portfolios. That way each portfolio can be managed separately.
In order to create multiple portfolios, use the "Manage Portfolios" button found at the top of the "Dashboard". The dialog that pops up is how you can create new portfolios, transfer funds between portfolios, and manage which funds are held in which portfolio.
After selecting "Manage Portfolios" you will see the following dialog.
You can freely move funds between these portfolios by selecting the portfolio you want to move funds from.
Then select the portfolio you want to move funds to in the drop-down.
Finally, select the funds you want to transfer and click "Move Funds". This will move your funds into a separate portfolio.
When creating an automation, you can now prevent these funds from being automated by not attaching an automation to the portfolio you want to be excluded from Shrimpy.