So far, I'm happy with the repetier host, but a few things are not coming out right:

1. First few layers and last few layers have trouble bonding, resulting in the faces of the prints wanting to peel off.

2. The last layer (which is a flat face) comes out patchy with small holes in the print.

3. The print is centered on the repetier host, but the object is printed very closely to the edge when it transfers to the computer.

Also, how do you change the settings of the honeycomb patter? Do i have to open slic3r as an independent app?

Any highly reccomended settings that I should use?

answer to question 1: and 2:
   increase extruder multiplier in slic3r
experiment with it ....set for example to 1.1

Another issue is that, even though the object is centered in the software, the last print I did ran off the right side of the briny bed. Is there a way I can calibrate this better in settings?

Did you ever fix this problem?  I am having the same issue......

Thanks

So is it difficult to set the home as the correct 0,0 point? If it's too much work, would setting the dimensions to 240x240 stretch passed the 200,200 mark? Or will placing the object to the front left be the perfect position to start the print?

Yes, that will work as a temp solution.

BUT!!!

Be careful since you still only have a 200x200 print area you could inadvertently slice a larger model then the bed could fit.

1. First few layers and last few layers have trouble bonding, resulting in the faces of the prints wanting to peel off.

2. The last layer (which is a flat face) comes out patchy with small holes in the print.

3. The print is centered on the repetier host, but the object is printed very closely to the edge when it transfers to the computer.

Also, how do you change the settings of the honeycomb patter? Do i have to open slic3r as an independent app?

Any highly reccomended settings that I should use?