I usually take off from a bow cushion when there is room (I.e., no one taking up the center aisle / only two people sitting at the sides of the bow). It also fits between the seats when the bow cushion is not installed but if you take off from or land there do it quickly so it doesn't hit the seats or anything on the way up or down. If the bow is full I will take off from the top step of the swim deck unless the water is rough or I want to take off while the boat is underway in which case I will launch it from my right (non - throttle stick hand). So where / how I take off really depends on the situation. Unless the boat is anchored I will usually just hover it to head height and recover it by hand while the boat is drifting or anchored but prefer to let a friend or family member "in the know" grab it out of the air by the bottom of the skids with both hands.
What helps me is the addition of blade guards (no string between them). That is, I feel more comfortable flying out of and moreover into the boat and near people with the guards on. For $20 they give me a lot of peace of mind.
Here is a video of two of my early take offs and Landings from the bow when I was boating alone.
Soap box time so stop reading if you are not interested in my perspective on flying rc models.
I can't emphasize the next point enough, do not become too reliant on the GPS assist functions or the advanced flight modes of the phantom or any rc helicopter for that matter. Most of the flyaways and crashes I've read about involve operators that haven't mastered basic radio controlled model flight skills. That is, they don't know how to determine which way the heli is pointed/oriented when it is hundreds of feet out or up so when they try and fly it back it doesn't do what they expect. Some rely on the advanced flight mode so it doesn't matter which way it's oriented but they haven't practiced using this mode so they don't activate/deactivate it correctly or just use it incorrectly. That is they forget that in this mode GPS stabilization may be off so the inherently stable multi copter (which bormally hovers hands free of the remote) will continue to drift in the last direction it was headed until an opposite directional input is made on one of the control sticks.
To counter this, what I call over reliance on tech, I recommend that all people new to rc helis (conventional pod and boom and multi rotors) simply practice flying low (about 30 feet high) and close (at least 30 feet out). The starting position is with the operator facing the rear of the heli. On the phantom the green lights are mounted on the back and the red on the front. From this position left on the left stick will make the heli yaw / point to the left and right when the stick is moved to the right. The right stick will also make the heli move in the direction its pointed (I.e., roll / slide left or right when the stick is pushed left or right and pitch back and forth when the stick is moved back or forward). This is all basic stuff but mastering or at least being aware of your position relative to the model's is key to controlled flight. From the tail in hover position get used to moving forward, back, left, right and rotating all within a 10 foot square over a 4 foot square target and always ending in the same position you started in (that is tail in or you facing the tail of the heli). Once you are comfortable with this practice flying. In short, medium and large circles, first clock wise than counter clock wise. After getting the hang of this do some figure 8s and finally end with some nose in hovering (wherein all the controls are reversed). With multi copters all of this can be done in as little as one battery's charge (20 minutes) and can really help in a pinch, like when the heli is too far out to see the lights on it. Don't freak out or instantly hit the return to home function which won't work they way you need it to when you have moved away from the home/take off point. Just move the right stick to figure out which way the heli is pointed, reorient the heli so it's tail in and fly it back, like a boss. If you do plan to use the return to home function don't forget to set the return height appropriately. You need to clear trees, power lines and buildings but don't set it so high that it violates the fcc's 400 foot maximum and possibly gets into the airspace of full scale planes and helis like police copters (like the guy in this story did, he is lucky he didn't get fined almost $28k :
http://www.ktvu.com/news/58030706-story ).
Lastly consider joining a forum similar to this one. Here is one that I registered for which is dedicated to phantom owners/operators.
http://www.phantompilots.com