It seems that you have several problems with codecs, settings and also with getting the right tools.
I know how is to be on tight budget, so, here's my input:
If you are familiar with FL Studio but not able to buy it yet, then when you export songs, export tracks separately (there is this option) so later you can import the wav files in a program and edit them.
Get familiar with some programs that are free or offer an unexpiring unlimited demo. There are quite a few, Podium Free, Reaper, MuLab. Get your hands on Audacity and learn how to use it, you'll always need a sound editing program and this one is good and free. FL Studio can import mp3, so, convert the watermark as mp3, or eventually mix the watermark in another program (Audacity?).