Excelent question, I was wondering that same thing about the mulm. I personally added it on top of the peat. I don't think it was all that effective for me beacuse my substrate goes from 3 1/2 inches to 5 inches deep. So, when I planted I don't think the plant roots actually came in contact with the mulm/peat, and I think it was a little deep for effectively starting the biological processes in the substrate. Oh well, live and learn. One thing that has helped me with new tank syndrome a lot is using "aged" water and filters. I run all my new filters on a healthy tank for a month or more before setting up a new tank. Also, I use at least half of the new tank volume of water taken from that same healthy tank. Seems to really cut down on the algae blooms from the cycling process.
BTW- I agree with the above Flourite/Onyx is the best choice for a new plant tank. I have it in two tanks (4years and 1 year old), and it seems to be great. I went budget on one tank and used Schultz's CSC(very cheap $12 for 40#'s) capped with fine gravel and the plants seem to like it, but it's too light. I suck a lot out when cleaning.