IRA means individual retirement arrangement. You have one arrangement, no matter how many accounts it is split into. You do not need to track the basis separately, just note the total amount of contributions made to any Roth IRA.
In your case, you have made $150,000 of conversions, that is your conversion basis. You apparently have no contribution basis. If you withdrew $41K, your remaining conversion basis is $109K.
Turbotax should track that correctly, maybe you confused the program by trying to keep the account separate. In any case, if you are audited, you need your own accurate records of your conversions (form 5498, probably)--nothing you entered in Turbotax will be convincing to the IRS since you could type anything into the program that you wanted to, even if it was not true.
