Most airlines would recommend that you get seperate coupons. This shouldn't cost more (i'm pretty sure) and would be in your best interest. If you are good they will pull both, if you get stuck then at least you aren't left with nothing!

I know QF always recommend that one gets a MEL-AKL and AKL-LAX coupon on their service that transits AKL (if i had the desire to try the AKL transit flight rather than direct... which i certainly don't!) rather than the MEL-LAX coupon.

I know at CX we recommend everyone gets a HKG-ADL and ADL-MEL ticket if planning to catch our transit flight (CX105). In reality there is a a 99.99% guarantee you would not get bumped in ADL - but they still recommend it.