First beware that the Pi-3 uses the UART for wireless.
This means you can't use wireless if you want to interface with the Gertbot at the same time.
Use a Pi-2 instead.
I know nothing of analogue trains but if they have DC motors you can use 'brushed mode' to control up to four trains/tracks individually.
As to I2C: the Gertbot does not use the I2C interface so it is available.
But when you plug a Gertbot on top of the Pi, it goes over he I2C pins. Thus some sort of adaptor cable
or soldering two wires to the I2C interface is required.
The Gertbot is a DCC source. Thus it generates the DCC signals which both powers the tracks and
transmits commands. You need locs with DCC decoders to make use of that.
As the four channels of the Gertbot can be set up individually you can e.g. set one to DCC mode and still have three left
for DC tracks.
DCC has been tweaked so that it can produce a DC level but all DCC documents I could find told me it was NOT recommended.
The DC mode is implemented and present in the DCC command as parameter,
but I never had the locs to test it so in the manual it is marked as 'under development'.
(Development means to me design and test. As long as it has not been tested it is thus theoretically under development

)
I hope this answers all your questions. If not send me a PM.
(I assume you are the H.H which send me an email. I prefer to answer here so others can benefit.
Other tip: post questions about Gertbot in the gertboard-classic section please. I keep a close eye on that).