Since Shapeshift processes trades right from the wallets, there is no easy import solution for it.

 There are several possibilities to keep track of Shapeshift transactions.

 1. Just enter the trade as deposits and withdrawals from the certain accounts. Unfortunately it is not possible to generate a proper cost basis this way, because there was no real "trade", just some IN and OUT book sets.

 2. Open up a new account and link it with your current one. Then enter all your trades from Shapeshift. This way you could use all tracking features without messing up your balance and without automatically overwrite respectively add trades via the automatic import.

 3. Treat it like an imaginary exchange. This is my recommended way of handling Shapeshift transactions.
 You add the INs and OUTs for every single trade from SS on the involved exchanges and you do a trade on virtual Shapeshift exchange. For example:

 - OUT from "Wallet A" (included in automatic imports)
 - IN on "Exchange Shapeshift"
 - Trade on "Exchange Shapeshift"
 - OUT from "Exchange Shapeshift"
 - IN on "Wallet B" (included in automatic imports)

 This is a more complex way, but it would represent the transaction perfectly. It would be the best solution if you need to view your data accurately in all analyzing tools and also to separate specific exchange data.