Corrosion!

I have a 2001 Compass Cruiser, just been serviced, new exhaust & brake pipes and chassis sprayed, but while it was up on the ramp we noticed 2 small patches of decay in the wooden underfloor just where it meets the cab. Any suggestions for treating? I'd thought of using a wood hardener followed by a filler. Should I use a preservative on the rest of the floor?
Jmax

I guess you have to do a bit of investigation and a few problems to resolve.

Is the damage confined to the lower sheeting?
Could the upper layer of the wood-Insulation-wood sandwich be damaged?
Can you identify the source of the water/moisture?
Can you get to the rot and kill the bugs that are causing the disintegration of the wood?
What level of damage has been done to the structural integrity of the damaged wood? (plywood, I guess)
Is it possible to replace the whole of the panel, without major surgery on the vehicle?
If not can you replace a section of the wood and find appropriate structural support for the new wood, without major surgery?
Can you repair it?

Personally I would consider repair before replace, (i)you seem to have found this problem early (ii) there is only a small area of damage (iii) you avoid lots surgery that may, on balance, be more harm than good (iv) if your repair fails you can still replace the damaged sheeting

Once you start cutting the floor sandwich there is no going back.

You could consider treating the wood to kill the rot with wood preservative -penetration is the key to success. Ethylene Glycol (POISON) or antifreeze is good for wood rot treatment.

There are a number of penetrating epoxy brands available.
West GFlex 660 can be used in wet conditions, so may be worth considering.
If you can get the epoxy into the plywood lamination layers, by drilling holes through the bottom layer and injecting "thin" or "watery" epoxy to allow good penetration (epoxy can be diluted with solvents) you may kill several birds with one stone. You Re-glue the wood laminate layers, prevent further damage and add structural strength to the damaged wood.

After some time when you are satisfied that the repair has worked successfully you can add a layer or layers of Fibreglass over the damaged area to make it stronger than the original.
Then add under-body seal.

No doubt others will have other, perhaps better, suggestions.
Good luck with the job. Do let us know how you get on.