There are a couple of standard ways to deal with the water (and pressure)issues, one common approch is to build a metal pressure vessel that houses all the doings with wiring passed thru connectors designed to take the pressure (Or cables fitted with water blocks, be careful here below 100m or so the water will quite happily flood the pressure pot by flowing up the inside of the outer sheaf of a cable).
There are a couple of thngs to note about this approach, formost being that if you do have the pressure pot flood due to a small leak and you then bring the thing back to the surface you have just created a bomb as the internal pressure may still be many atmospheres in the small volume of high pressure air trapped above the water, a pressure relief valve is a good thing.
The next approach is to fill the housing with oil which helps with both cooling and can optionally be pressure compensated such that the internal pressure matches that of the water, good for shallow water work (But messy to work on), you quickly find out which parts have voids inside if you send such a thing down to a few km.
The final common approach is to pot everything in PU, same issues with voids but if you do the prep on the wiring right (the PU MUST bond to the wires) it will be watertight.
You will get real good at inspecting O rings and thier grooves if you go into this stuff.
Now, control is best done with a wire unless you are determined to go autonomous (and those guys regularly loose vehicles, you have been warned), but any such wire must be close to neutrally boyant or it will become an issue, also the voltage drop due to the resistance of a km or so of cable can be a real pain, lots of volts up on deck is the typical answer.
You can get off the shelf cables for this stuff which have a couple of power cores and a pair of fibres which is increasingly how the ROV game is going, put an ethernet switch on the vehicle and you have loads of bandwidth for video, sonar (Generally more useful then video), telemetry and telecommand.
Regards, Dan (Who used to do sonar for a living).