I think the easiest thing is to use the Cura application together with CuraEngine.
If your printer is not supported, you'll need to add it manually by adding a JSON here: https://github.com/Ultimaker/Cura/tree/master/resources/machines
But when you are done you can easily choose all the features you want. For example: generating supports, printing order when printing multiple models, etc.
Cura and CuraEngine are developed at the same time, so you can expect that all features supported by the engine are accessible by the UI.

I'm not sure if it's possible, but on github is code for setting CuraEngine up. Maybe you'll find this link, CuraEngine/src/settings/settings.cpp helpful.

The latest release has more speed customization. You can change first layer speed, outer shell speed, inner shell speed, infill speed, and top and bottom speed.

You can cut objects, its just a little wonky. In the advanced tab there is a "cut off object at Z height" that you can use to cut objects in half.

Theoretically, you can put all settings into a JSON formatted file.

First, try

CuraEngine.exe --help

The proper way is to first load in settings from the .def.json file of your printer. However, the formulae in the machine definition file are not being processed. CuraEngine only uses the default_value.

Then you specify setting overrides to set specific settings to a specific value. The specified settings are applied to the last provided object/extruder and otherwise globally.

CuraEngine.exe -v -j machine.def.json -s global_setting=global_value 
    -e1 -s setting=extruder_value
    -l object_to_be_printed_with_second_extruder.stl -s setting=object_value 
    -o output.gcode

One-at-a-time mode is done by adding --next commands between each group:

CuraEngine [general settings] -g [settings for the first model] --next [settings for the next model]