Sea Foam dates back to when carburetors were the norm. They do have a very mature formula, but it's actually a bit aggressive on a fuel injection system IMO. Better off having a shop run some 3M (or similar) cleaner through the pressure test port on the rail, works better than anything. If you really want to use the Sea Foam you can run it through they gas, or suck it in through any line that will feed into all four holes, a vacuum line on the manifold works well. It does make a smoke screen though. I've actually done that on my 1.6 when it was running funny, it cleared it up but also tripped an 02 code on the #1 sensor. Best of luck to you.
-glahti