This should be a quick one. If I wire two 12V batteries together as follows: + to + and - to - then connect one battery to amps. This would not run the batteries at 24V correct?

Correct, it would double your reserve and cranking amps but not increase your voltage. So with them wired as you have stated you would still be at 12v

how would that effect charging from the alternator?Or would it?

It would put more of a load on the alternator when they are drained. It would help though if you have a large amp or some other power source that takes ALOT of power in short bursts. The additional battery will help "absorb" this shock which can make alternators heat up and create a faster failure. The batteries will not charge as quickly but at the same time, they wont discharge as fast either.

Thanks Trevor, any suggestions on how to set this up so things work good and last as long as possible?

It depends why your adding the additional battery. I would recommend a battery isolator or battery selector switch. This way you can completly disconnect the batteries or you can isolate the batteries so that if you run one down it will not leave you stranded. A switch also makes it nice for storage, as this allows you to disconnect the batteries from the system without any tools. I personally use the Perko brand switch and purchased off ebay for about $30.

I second Trevor. I am using a combiner and don't have to touch a switch. you can use them with a perko if you like for emergencies. I am using it with 3 batteries and it is keeping up really well. Lot's of combiners to choose from