For the amount of CNC work that I do I don't bother with fixturing, just bear in mind how I will hold a part when doing the cam to make sure nothing gets hit.

I've not found personal use that restrictive, I just play about with stay down distance and percentage and also the non engaged feed rate and that goes a long way for compensation for the loss of rapids, plus I try to use a decent feed rate which it defaults to as the rapid rate.

I confess to being a beginner with CNC – but re the above posts about editing the Gcode files – I ran into a similar problem (odd 'boxes' appearing in the Gcode) and had to edit the sequences which cut these boxes out. I use Linux, and tools like Candle2 or UGS have a 'visualization' of the Gcode showing tool paths which allow fairly easy analysis of what is going on, but they usually require the machine to be connected and/or running. There is also a tool called 'Camotics' which is primarily intended to drive a proprietary CNC machine, but it will allow visualization without being connected to the machine. It will run under Linux or Windows.

No connection with any of the above software, except as a user

I do it more or less as Emgee says which for our often one off jobs is fine.

I feel modelling all the vices, clamps and fixtures is more of use to commercial users where they may have several parts on the table at once to save having to keep stopping and starting and reduce tool changing times, even more so when using 3+2 or 5 axis where you do need to be even more carful as the trunnion swings about.

Emgee mentions safe height, yes you could probably save a few seconds by not having the tool lift so far above the work and only lifting higher to clear a fixture but would it entail the same or more work modeling the positions of the clamps etc and then making sure you actually use them on the machine in the position you have modelled them? Unlikely for a one off but for production runs of several 100 parts then yes it's probably worth the effort as time is money. You will also need to model the tool holder and set stickout from holder for each tool to make full use as it's not going to work if the machine keeps the cutter clear but drives the tool holder into a clamp or stud

If I've got cap head screws holding the work down then I will stick with F360 default 10mmclearance and 5mm retract height, if it's in the vice then drop it down to say 8mm and 4mm and just make sure there is more material sticking up above the vice than my work top height to lowest bottom height

For sheet work then I just make sure any clamps may will be outside the simulated part or set the tool ctr to only just go beyond the bounary of the work and use tabs or screws if there are hole sin the part to stop it moving once the outside is cut.