There won't be much of a difference between the two source materials if it's only nndmt in your mix. The only thing I can think of is that acacia tends to have a higher amount nmt, which to my knowledge is the source of the "gooing" or "gunking" you'll sometimes see with acacia confusa, it's the stuff that kind of looks like marijuana wax.
Anyway, you might as well mix the two together if you have them handy. Rubbing alcohol (91% or higher) is pretty good at dissolving both nndmt and nmt, but has trouble with the harmalas/harmines that come from either caapi or syrian rue. I can't comment on how to go about dissolving harmalas properly since I usually make 10x leaf with my changa.
To make that, you take 10 grams of caapi leaf, simmer it (almost boiling, but not quite) in half a pot of water until it's down to about a half a cup to a cup. Then strain the water from the leaves using either a thin cotton t-shirt or with a good sieve. Finally, put 1g of fresh caapi leaves into that half cup of water and allow it to evaporate under a fan/on a windowsill.
I've smoked/vaped them using regular nndmt crystal mixed with the acacia goo, and the only differences I noticed from plain nndmt is that there was more of a body buzz that lasted for about an hour after the experience was over.
That said, my favourite mix for changa is - .8g 10x caapi, .2g blue lotus petals, 1g nndmt.
Good luck and happy travels!