As long as you do not turn auto-sync on, or synchronize these positions manually, CH will leave these positions alone.
If you do synchronize these positions you can also select them and press ''hold''. In order to see the correct percentage profit, you will have to look up the rate at which you bought these positions on your exchange's trade history, and fill in this rate when you synchronize the position.
You can find this synchronize button on the bottom right of your dashboard, underneath current assets.
