I have done some thinking along these lines as well. In fact I essentially have 5 accounts. A brokerage account (non-ira, taxable) and 4 ira accounts, two traditional and two Roth, one of each for me and my wife. As to your question, There are a number of ways you can do it, and truthfully I have tried most of them.
You can manage each independently.
You can manage them together as one portfolio matching holdings in each.
You can manage them all together as one portfolio, not worrying about what is in which account.
You can manage them all together as one portfolio, and specifically put the riskier, higher potential stocks in one instead of another.
But honestly in the end, I have decided that there are big differences between the tax exempt and the non-tax exempt in terms of how you treat them, but not really much between the traditional, Roth or 401k accounts.
Here are the important differences between taxed and tax-exempt accounts:
Ordinary High dividend paying stocks should be held in a taxable account since the tax treatment of a dividend is better than ordinary income, i.e. Less advantage to protect that income.
REITs and other non-ordinary dividend stacks should be held in tax protected accounts since they are taxed as ordinary income.
Any stock that could be a short term trade (held less than a year) should be held in a tax protected account.
Any stock that is expected to be held for a very long time, I hold in my taxed account.
So, how do I handle things now…
In my taxed account, I look for long term “buy and forget” type companies. I don’t want to trade stocks in this account. I look for ordinary dividend payers and companies that I think will grow for 10 years or more. If I owned an S&P index fund, I would own it here since these vehicles are very tax efficient.
In my ira type accounts, I hold any REITs, I hold growth companies that I am not sure how long I will hold as well as low dividend high growth companies. If I owned a managed mutual fund, I would own it here as I don’t have to worry about the tax implications of the annual payouts.
Overall, I look at all my iras as one account, with different stocks in different accounts, but I have used individual accounts to try out different investment philosophies to compare to the overall return…