Which Ardupilot for my 3 different RC models?

I am newbie on autopilot, but I am flying FPV. I already do have an Remzibi 3DR OSD and NMEA GPS.
I am planning to buy a ArduPilot for using independently on one of my 3 RC models: electric 2m glider, 450 (electric) classic helicopter, electric boat.
My 450 Helicopter has already a Flymentor stabilizing system.

I did find 2(3) different models of ArduPilot: ArduPilot w/ ATMega328  - $24.95 and ArduPilot Mega (1280/2560) - $59.95/$64.00
Looking at features I did notice the differences between them are related to number of analog/digital inputs, number of RC-in channels, memory, size.
Also I did notice that ArduPilot w/ ATMega328  uses Config Tool (1.4.14) IDE for missions, comparing to ArduPilot Mega (1280/2560) which uses Misison Planner (1.1.42) IDE.
I did notice the missions (txt file) are not compatible between those IDE, the format is different, indeed.

My question is next: Which of those ArduPilot I can use to incorporate on each my 3 models?  I am looking for a simple setup, low budget.

My radio control is a 6 channel (DX6i). I am OK with programming/soldering.

Chris

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