I'm sure there are a lot of people out there who start out with some grand arrangement vision in mind and can sketch it out from the get go. Personally I can't work like that at all and I don't think I'm alone. I work very haphazardly, organically, whimsically, scatterbrainedly, call it what you will.
I usually start with some riff, beat or other simple musical idea that I've come up with while messing around. And then I build around it slowly, adding bits here and there and experimenting with different directions. Very often during the course of a project I will do a complete about turn and revamp the whole thing into something completely different from my original idea. Sometimes this will result from a particular sound not working out in the mix - I'll change it to something else and realize that this new sound suggests a completely different style, so I'll change the beats as well. And sometimes new sounds suggest different arrangement directions.
Sometimes a musical idea you originally thought would be the "centerpiece" of your song gets relegated to a less dominant role in the course of the organic development of the project. For instance I'm currently working on a remix of a song by a female vocalist. All I have was the bare vocal part. I originally came up with a guitar riff that I thought was awesome (still do). So I set about trying to arrange the tune around this riff. A couple of months later and the guitar riff has found itself in a back seat position, near the end of the song in the final verse. I had come up with better sounding synth parts in the meantime which I realized should define the song more than the guitar riff. So now the riff is just adding a bit of variety toward the end.
If you work like this, you have to be proficient in a few things. The first involves being intimately familiar with the arrangement editing tools of your DAW. How to move chunks around, how to delete time, how to make sure automation moves with clips etc. The second involves learning to let go of musical ideas which aren't working in the track. I know I find that part hard. But set them aside and know they're always there as raw material to take advantage of in future projects.
As for FX, I don't think there's any harm in working on a rough mix at the same time as your arrangement. I sure do. I know there are people who get the whole tracking thing done before they insert a single plug, but I can't work like that. My musical/arrangement decisions are very much influenced by the sounds I'm working with, and I need to use a rough mix to get an idea of whether or not sounds will work together. If you can't get them to sound good in a rough mix, time to choose other sounds. I'm sure most EDM producers are playing with FX as they write. How on earth can you figure out the arrangement of an EDM track without FX and automation, when things like delay and filter sweeps are an integral part of that arrangement?
Most of all, just accept the fact that there's no hurry. Sometimes you need to perform multiple "passes" of a project, whittling down and editing and rearranging parts, before a good arrangement emerges. Depending on how you work (and how many hours you have), this can take months. But even if you choose to set it aside to work on other projects, make sure you come back to it regularly so you don't lose sight of it. I've come back to projects after a year and have no freaking clue at all what I was doing with the arrangement and routing etc. Very easy to abandon projects when you just don't recognize them anymore!