With my mk2 estate I have a full size 16" spare wheel. The dealer has advised me to keep it as it will fit the mk3. Is this the case? My new one is a SE L estate.

Yes, it should be fine, the bolt pattern and rolling radius are the same. Only the VRS needs a 17.

How different is the underboot storage, will the mk2 polystyrene fit in the mk3 (i dont mind minor modification)

The mkII jack won't fit the mkIII though.

The mkII jack won't fit the mkIII though.

I'll look on ebay for a jack then, cheers

The spare jack kit which includes the nut to lock the wheel to the floor of the boot is 5E0093860. The link below is for the OEM part:

 

http://www.skodaparts.com/product/octavia-a7-spare-wheel-tool-kit-2014-2018-50761

 

I bought it for my Elegance but I also bought the wheel too:

 

http://www.skodaparts.com/product/octavia-spare-wheel-2014-2017-50745

Thanks for the links I'll save them for if it doesn't fit well enough

With my mk2 estate I have a full size 16" spare wheel. The dealer has advised me to keep it as it will fit the mk3. Is this the case? My new one is a SE L estate.

Did you go for the 16" wheel option when you ordered your car. The correct spare for a 17" shod SEL is not a full size 16" spare - it is also speed restricted. If you look at the online configurator there are 2 choices of spare and these are matched with the rim size selected.

I have gone for 17", im aware that the configurator spare is a space saver. Surely a full size wheel is safer? Thats why I wanted to use my full size if possible.

I thought for the O3 the 17 was a skinny wheel and the 16 was a full size?

I thought for the O3 the 17 was a skinny wheel and the 16 was a full size?

That is correct

Maybe I haven't been clear enough.

I know that if I order a new spare, it will be a space saver.

I already have a full size 16" from my mk2

My question was will this fit? Will it fit in the boot correctly? What problems os it likely to cause?

Legally a 16" spare would be treated as a space saver, restricting you to 50 mph, as it's a different size to your other wheels.  It might be marginally 'better' than a skinny space saver to use though.  It should fit, same bolt pattern and close enough off set.