[tucsonjwt]

Either way will work. I ran both positive and negative cables through holes in the radiator core support and tie wrapped the cables to the underside of the radiator top panel, so the cables are out of sight.
You might want to check out a high output alternator, but you should also have heavier cables if you install one. Heavier cables for the battery and to the starter are also a good idea.
Two batteries will cost more than you might think: You should buy two new batteries or the old one will bring down the charge in the new one. You will need a battery tray for the second battery - the OEM ones are pricey but are way better than the aftermarket ones. You will need the extra set of cables and post adapters.
If you drive your truck a lot you will successfully keep a charge on two batteries. If you don't drive your truck much (like me) you will have difficulty keeping one battery well charged, much less two batteries. This is where the high output alternator comes in. You can search the internet for high output alternator and get advice on this, mostly from h.o. alternator vendors and car audio sites. Still, a high output alternator puts out most of its amps at higher RPMs, so city driving alone will not produce a lot of amps.
I have a high output alternator (140 amp, I think) and I find that for some reason the primary battery gets most of the charge and the secondary battery gets less of a charge - I have no isolator between them, which would be designed to charge the primary battery first, then the secondary battery. If you want info on isolators you can search that on the internet also, but I don't like isolators. I used a Ford solenoid between the two batteries instead of an isolator when my isolators kept failing. I had a toggle switch on the dash at one time to use two batteries for start up, but I don't think that is necessary.
Bottom line, two batteries ultimately won't help you much in the long run if you are providing the same amount of current as you were to one battery - you will just have two batteries with the same level of charge instead of one battery. Again, if you drive your truck a lot you will keep a good charge on both batteries, even with a stock alternator.