Slicer setting/compatibility questions

Okay, so with the initial testing of my Duet powered printer complete and pretty much satisfactory, it's time to run some plastic through this thing.

I hadn't given it much thought up 'til now, but this process has taught me maybe just enough to worry about gcode flavor when it comes to things that might go wrong.

To date, my printers have run Marlin in carious iterations, and Slic3r has a "Marlin flavour" setting for generating gcode, and that's what I've always used. I have Cura installed on the system that I do my slicing on, but I've never actually used it. Those are probably going to be my choices.

I'm sure that people have their preferences. I'm also pretty sure that most of the gcode is going to be the same. It's not like I'm dealing with multiple extruders or really anything that isn't fairly basic when it comes to how this all starts, so probably the custom start/end code sections of Slic3r will be more than enough to ensure that I don't have too much trouble with getting a print out.

That said, are there specific settings for either Slic3r or Cura that will make this whole thing go more smoothly?

As said, I haven't actually used Cura. I know that Slic3r has the ability to keep profiles for more than one printer, and that's going to be important to me. I assume that Cura can do the same thing?

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MBot3D Printer
MakerBot clone Kit from Amazon
Added heated bed.

Leadscrew self-built printer (in progress)
Duet Wifi, Precision Piezo parts

Set Slic3r to output Marlin-flavour and tell Duet to act like Marlin.

M555 P2 ; Set output to look like Marlin

The rest is in the start/end code as you said.

I don't think that's quite accurate. Setting RepRap to emulate Marlin refers to how it formats it's responses to console commands for compatibility with USB control software which expect responses to match what Marlin would respond with. It has nothing to do with the slicer as far as I'm aware.

The slicer setting to change gcode flavor on the other hand can have some actual consequences for instance reprap and marlin use different means of setting acceleration and jerk parameters, so you'd want the slicer to use the RepRap flavor. Recently Reprapfirmware has had some of the alternate marlin commands implemented, so it will accept both, but better to stick with reprap flavor anyway.