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How do I charge two battery banks and still keep them separate? 

There are a number of ways of doing this:

• The simplest way, if you can remember to do it, is to turn your battery switch to "BOTH" when charging, and turn it back to 1 or 2 when you are finished.  This solution is unsatisfactory for those who sometimes forget and then end up with a flat battery from time to time. If you want to automate the process and make it idiot proof, then you need to pick one of the other options. 
• The best way, if you can manage it, is to have two alternators.  This allows independent charging of each bank, and by fitting a combiner switch you get the added feature of a backup alternator for either bank in the event of a failure.
• The old fashioned way was to use a battery isolator, which is a set of diodes which allow the charge to go to each battery but doesn't allow the batteries to connect to each other.  One problem is that there is a voltage drop across the isolator means you need to have an externally regulated alternator with a voltage sense wire downstream of the isolator.  Another problem is the high failure rate of isolators. Another is that the voltage drop means wasted energy.
• A popular and successful way is to use a battery combiner such as the Blue Sea ACR  This is a solenoid which connects the batteries together when they are being charged and separates them when they are being discharged. 
• The last way is perhaps the most satisfactory. Using either the Xantrex Echo Charge or the Balmar Duo Charge you can charge the start battery from the house bank. These relatively simple devices give a controlled amount of charge whenever the house bank is receiving a charge.

Should I hook up batteries in Parallel or keep them in separate banks?

How big a battery bank do I need?

For most people to answer to this is "as big as possible".  Charlie Wing's book the "Boatowners Illustrated handbook of Wiring"  has a very good explanation of how to calculate the capacity you need. The calculations start by working out what your daily load will be both at anchor and while underway.

You need to remember that you cannot use all of the capacity your batteries have without shortening their life considerably.  You should aim to not discharge your batteries past 50% of their capacity.  In addition if you are charging batteries from your alternator while underway you will find that the last 20% of the charging cycle is painfully slow.  All of this means that the amount you have to work with for continued operation while underway is 30% of the rated capacity of your batteries. 

So for example to provide for a consumption of 100 Amp Hours per day and charge once per day you would need to have a battery bank rated at  333 Amp Hours.  

I enclose a sample table below for you to complete in order to calculate what your actual power consumption is..  I have filled in a couple of lines with a hypothetical example.  Every boat will be different of course and you will have to make a best guess at the answers.  You should do a separate table for when underway.  Often at anchor the loads will be higher as there are more lights left on for longer times and they are not offset enough by lower navigational equipment loads.

Does anyone out there know where I can find a 'complete' listing of battery dimensions according to group or whatever?  I have a French built boat and cannot find anything to tell me what US equal size mine are.  It really matters when your battery boxes are as tight a fit in the scheme of things as ours are.

The Battery Replacement Data Book is a free publication published by Battery Council International of 401 N. Michigan Ave, Chicago IL 60611  and you should be able to get a copy from your local battery shop, I did. It gives dimensions for the common group sizes, but it is aimed at automotive uses and there are many batteries out there that are not standard. For those you will have to check with the various manufacturers

Nominal dimensions for common sizes are as follows: