Just to clarify, I set-up my CNN portfolio manually. It is actually designed to be linked to your brokerage accounts. If it is linked it will update automatically with any changes and will probably track cost basis. I don't like linking anything to my brokerage accounts. I just don't trust the internet that much! The CNN portfolio is run by SigFig so it might be better to use the SigFig portfolio and cut out the middle man.
I tried the CNN website too, and it's really easy to link to your brokerage sites and download data from there. So I linked to TDAmeritrade and my 1000 KMI warrants at $4.36/share were listed as being worth $436/share, totally skewing my numbers. I reported this to them and they (sigfig) said they're looking into it.
I started a longer process of linking to TradeKing, and TradeKing said that by authorizing access to SigFig via the API, I was giving them the right to trade in my account as well as view it. That was a bit too scary for me, so I said no and closed my CNN account.
I do like the FT portfolio manager on the whole, but it handles dividends in a difficult manner. Besides the issue with mixing Reinvested Dividends and Cash Dividends in a single stock's history not being possible, the dividend information it uses appears to be the ex-dividend date and therefore the ex-dividend stock price, rather than the pay date and the pay date price. This means that you'll end up with a different number of shares (assuming reinvested dividends) than you really have and there's no way to adjust it.