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What if the 2 startups are complementary?

Like say, you are doing a dating site and a social networking site, which was the case for Intermix Media, parent of Myspace

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Then run them as one company so you can spend half as much time talking to VCs.

That's what I'd do if I was in that situation... structure it as separate holding companies for the IP or whatever so you can flip each product individually if needed, but don't unnecessarily duplicate resources. Of course you're probably going to get into a world of fun "internal accounting" taking this approach... you will probably want to "bill" the appropriate holding company for time spent working on that project, etc.

You only really need to do enough accounting in order to pay your taxes correctly. You might need more than that if you want to try to go public, but the rest can be repaired retroactively. And if you just sit down with the relevant IRS publications and read through them, you'll find that the tax code isn't as scary as you think it is. A tax return is about as complex as, and makes about as much sense as, a typical Microsoft API.

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