IRA Account Advice

Hi - Need some advice from the experts. I'm using Quicken 2004 Deluxe to track several mutual fund accounts, primarily to take advantage of Quicken's performance reports. I don't use it a lot and I'm not very well versed in Quicken. I need to set up a new account involving two mutual funds, held as a traditional IRA. Does it matter if I set it up using the IRA option for the new account, or just set it up as mutual fund accounts and mark them as tax-free? Any particular benefits to one of these choices? There's a possibility I will broaden the IRA to include a third mutual fund. Does that affect the decision which way to set it up? Thanks very much for your help, OC