Hey there! Glad to see you tried the tutorial out.
Two things.. the merge is part of the LOMO script.. when you run it you have choices, I almost always choose the options to work on a copy and to merge. Sorry that wasn't terribly clear. When you do it this way you see the result in a new canvas can you can then simply drag it over to the top of your working layer stack. In the tutorial, I did this twice and set one to overlay. However, all tutorials are guidelines and if you feel that this changes the effect too much then modify. That's just part of it.
I tell ya, its rare for me to follow a tut step by step and not add my own flavour to it.
Would love to see more attempts at this tutorial.