Shan I use to get water coming in from the well through the cable hole as the rubber boot doesn't seal properly,so i got a tube of sikaflex and filled it in.
Tape up the inside of the hole around the cables then fill the outside with siko,comes in white or black and dries like rubber.
Problem solvered.
However note:if you are getting water in the hull below deck this is another problem that needs to be looked at.

 Yeh only water in to deck  just seems like a stupid place to put hole too low in my opinion putting silicon in there is what has been done before so will do again cheers mate

Shane ,don't just use silicon ,use siko and clean the fiberglass around the hole with acetone so you get a good bond to the glass.

Sounds like the cable/hose hole is to low or the motor is heaver than boat design

motor cables should be at least 3 inches above the rear on the transom (lowest point) and well above drain hole but often installers route them lower to avoid bends/kinks in the cables.. want to rectify either way - either route it higher and seal hole (best solution) or seal as much as you can to lessen water coming in  _ i'd go the re-route myself - it is a potential boat sinking problem depending on a number of other factors (cockpit deck hatches and associate seals) bilge/battery capacity etc.

PS put up a pic showing the engine well depth etc before considering sealing it - ideally you want it draining for a reason - - Auto bilge in the engine well would be another option if sealing it but again not ideal (better than just sealing it) they drain for a reason.

PPS do you have basic fibreglassing skills if so there is a reasonably easy way to move the cable hole up.

i.e. Cut the hole upwards on both sides  into a new circle - so you end up with a oval shape (with the original circle/hole at the bottom and the new circle/hole (of same size) at the top) - pull/support the cables to the top of the "new hole" - flip the piece you cut out to the bottom and patch back in from the inside and gelcoat the well. then just have to put on a grommet (cut - put around cable and the glue/seal cut in grommet) and presto hole now higher.   :-)