My wife went out on her own last year (just celebrated the one-year anniversary), fulfilling a long-held dream of her's, which has been great.
Since she did an S-Corp, however, it added a bunch of extra complexity for our accountant. It was nice, however, to just pull all the personal stuff together (like I do each year), send it in, and watch them work through all the other stuff for a couple of weeks, safe in the knowledge that none of it was my problem.
In exiting her last employer, she got a decent equity payout, so we paid through the nose this year, but we had the amount set aside specifically for the purpose, so it's not like it was a surprise. Nothing like paying more in State tax for last year than I made, gross, in my first job out of graduate school. :O
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