roger - first try to discover why the wooden sill has rotted and fix this first; maybe overflowing gutter above (very common) causing water to cascade onto the frame.
If the whole sill has gone rotten then it needs to be replaced, trouble is getting an exact size match for your existing sill (probably imperial size) as the stuff now available is metric. Anyway, if you want to replace make one angled cut across the sill (why an angle? - enables you to lift one end of the sill out, a vertical cut would cause a jamb), then remove all the old stuff. Tip - before you do any of this secure the boxed frame to the wall with a couple of frame-fixings (access via the sash pockets). How to secure the new sill? - depends on the construction of your box-sashes. Obviously, you can't use any of the original joints, so one dodge is to fashion a couple of blocks (the size of the weight boxes), these are glued then lowered down the boxes below the weights 'till the rest on the new sill. Introduce screws through/into these blocks to hold the frame/sill as one. The sill can be fixed into the stone sill then careful use of frame sealant should make it weather-tight. Make sure that all old paint is burnt-off, good quality primer, couple of undercoats, gloss finish (only use oil-based paints for this type of work, although there maybe other posters who'll say water-based paints are OK - they aren't in my opinion).
Filling - use an epoxy filler not polyfiller/tetrion/etc.
