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.
I'm working as an employee for one startup and a founder of another, in two totally different business domains (financial software and internet games, respectively).
It's hard. Startups take more out of you than a regular job will, because you can't just switch into maintenance mode. There've been times where my boss has had a demo for an important client one week (making me work nights & weekends for a couple days to get it ready), and then I've gone straight to preparing a launch for the startup.
I don't think I really could've done it differently, though. I wanted to work at a startup so I could get experience & a sense of what I was getting myself into, and this is my first job since college. The day job is essentially funding my startup - it pays better than YCombinator, with similar advice & experience benefits. I thought about switching to a less intensive job at a big company, but I dunno if they'd hire me when I already have a startup on the side. Plus, I have a pretty good relationship with my boss and the IP policy is relatively lenient at my current employer, reducing the chance of IP problems (he doesn't care as long as I'm not starting a competitor, basically).
Overall, I wouldn't recommend it unless you're in a similar situation - first job out of college, self-funding, and want the training of a startup. If you're older and already have plenty of experience with business, I'd get a job at a big blue chip where nobody knows what anybody else is doing - a coworker said that Thomson Financial is great for this, almost everybody has their own private business that they run out of their cube because the company is incapable of getting anything done itself. If you can get YCombinator or similar funding, I'd take that: you're trading equity for time, which is usually a good tradeoff. If you can afford to, quit your day job and live off savings (I'll probably do this fairly soon, but I want a little more runway so my startup has a greater margin of safety).
On the other hand... maybe testing the waters with a few different things, and being flexible and willing to experiment might not be stupid. I'd guess that it's better to be sequential rather than parallel though, in order to focus on one thing at a time.
It's hard. ;-)
I'm running my own (small) business while working very hard at launching our startup. It's really hard, because you have so many people to keep satisfied (well, in my case at least); e.g. clients and partners.
But if you think you can do it....
Like say, you are doing a dating site and a social networking site, which was the case for Intermix Media, parent of Myspace