I have a project that i need to control my Quadcopter equipped with PIXHAWK (APM Fw), over Mavlink protocol. Basically i want to arm/disarm , take-off/land and give directions to quad to follow.

I won't use real GPS or RC Controller in my project. Everything must be done over Mavlink protocol.

In my project, i will also use a SBC (Pandaboard) and a Laser range finder sensor (Hokuyo URG) and do SLAM(Simultaneous localization and mapping) with it. So, i will have my quadcopter's position and environment map. 

I have 2 scenarios on this,

1 - If i know my quadcopter's position, can i basically tell my quadcopter that "hey you are at (x1,y1,z1) now. I want you to go (x2,y2,z2)" ? So i tought maybe i can fool my quadcopter with fake gps datas. Converting x1,y1,z1 to long,lat,altitude and feed my quadcopter with it continuously. By the mean time, i will give its goal position as a waypoint (converting x2,y2,z2 to long,lat,altitude). Is this possible ? Is there any better solution for this?
2 - If my first scenario is not possible, how can i basically tell my quadcopter to "go in +x direction, now stop, go +y direction etc.." ?
(my navigation, obstacle avoidance algorithms will run on my pandaboard, so i don't need my quadcopter to do any path planning or obstacle avoidance)

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