I have the same printer. However, I think I have a different version because mine is just unpainted laser cut wood and everyone else has one that is metal or painted wood. These are the settings I am using to control my printer. With this slicing software, you can use Cura, Slic3r, or Matter Slice. I use Matter Slice. I would play around the settings that I have attached. You are going to want to tune this to fit your printer better.
I have been getting some pretty good prints with these settings. You may want to change around layer height to fit what you need though. If you are trying to go for something that needs a lot of detail, try lowing the speeds of the print and increasing layer height. As for layer height. The lowest I have gone so far is 50 Microns. I have printed several prints at that quality and it is difficult to see the lines in the print.
The problem you are having is that the top faces are not closing. I have this set to 8 layers on the top and bottom and that has been working. You may be able to cut down on layers if you have a cooling fan that you can blow directly on the print. You may also want to try increasing infill to support the top layer.
With the configuration file, I need to let you know a few things. Under the Printer tab, and under Features. You can turn parts of the printer on and off. My heated build plate is currently not working so I have it turned off. If you have a heated build plate turn it on here. Also, please be careful on this screen. You may be able to do some damage to the printer on this screen.
Also, with the dual extrudes I am having some difficulty with them lining up. I think I have the offset set properly but I am not sure. The left extruder on my printer is jammed so I can’t really test it. However, I think I have the offset set properly. To change this got to the Printer tab, then to Extruder. Also, if you want to do an extended build plate with your printer, you can change that under the print area options.
If you have any problems with this file please let me know and I will help you out. To load this file you first need to add the FlashForge Creator Pro Dual printer using the add printer menu. Then click Settings & Controls, then click Options then import. This should change all your settings to match the file. Also, you will want to change your settings from Basic to Advanced to change some of the things I talked about previously.
For connecting to the printer, I can’t really help to much. I export my files to SD card and print directly from the printer. I do this because the USB connection on my printer does not work at all. So no Sailfish upgrade :(. Anyways, I have connected over USB with my M3D Micro and it works fairly well. You can set prints to email, and text you when they finish and you can monitor them online.
However, I would use this software to get you by. When you get a chance I recommend that you pickup Simplify3D. They do have a 30 day money back guarantee if you do not like the software. I agree though, I trial would give me a lot more trust in their software.
Also, here is the link to the config file. I had to put it in a zip because everywhere I uploaded it, it wanted to display as text instead of a file. Anyways, here is the link: https://dl.dropboxusercontent.com/u/229079674/CTC%20Bizer%20Config.zip