This link (same as above) talks about tax efficient placement of funds, and explains why the typical advice for bonds is to not put them in taxable (in short, because bonds pay monthly dividends, which are taxed at a higher rate):
http://www.bogleheads.org/wiki/Principles_of_tax-efficient_fund_placementBut then here's a link that says you're better off putting bonds in taxable only!
http://whitecoatinvestor.com/asset-location-bonds-go-in-taxable/I talk about this a bit in this thread:
http://forum.mrmoneymustache.com/investor-alley/which-vanguard-fund-for-emergency-fund/msg547482/#msg547482Long story short,
just keep things simple, and do whatever makes things easier for you. (Noticing a trend here?) If it makes you feel better to have bonds in taxable, because they will be a stable investment for you to withdraw to buy a house soon, or to keep the kid's money more diversified, then do it. If you'd rather avoid a tax bill now, then keep bonds out of taxable. It really won't make much of a difference over the long run. The more I read about this, the less it seems to matter, as long as your using Vanguard Total Market index funds, which are very tax efficient anyway.
Keeping this in mind:
1. Should I avoid bonds in my taxable account? There are plenty of good reasons to have bonds in taxable, and I think the purposeful silo-ing of money for children is a good one. Keeping things simple is another. Maximizing your tax-advantaged space by keeping more stocks in those accounts (instead of taxable) is yet another. I don't think bonds in taxable is something that should explicitly be avoided at all costs.
2. Should I save up and wait until I have $6000 ($3000 VTSAX and $3000 VGTSX) to contribute more funds to the account? If the money is to be invested anyway, the sooner you invest it the better. Don't let the money sit in a bank account until you can save up X amount to invest. I invest my surplus monthly.
3. Should I just save up $3000 and use VASGX and not worry about the fact I will have bonds in a taxable account? That's probably the best choice, keeps things simple, and based on your tax bracket you wouldn't benefit from municipal tax-free bonds anyway.
4. If I used VASGX for now since it would only require $3000, what would be the tax impacts if I wanted to split it into VTSAX and VGTSX once the balance was $6000? You can have a big tax bill, or you can have a $0 tax bill, or you can get a negative tax bill (a tax deduction). No way to tell without being able to predict the markets :) Why would you want to split it up when you get to $6000?
I know you're new to the investing world, and all the links and information can make things seem crazy and super-complicated. I stand by my earlier assertion that you're in a GREAT position! Don't be afraid of making a big mistake here. The things we're talking about here is small stuff, you've already passed the big hurdles. :)