I gained 3 points towards my dogs JW at the weekend but would like to know that can any points be carried over to Show Certificate of Merit award if I dont have enough by the 18 month mark

Not unless you won 3 Best of Breeds at the weekend. The Show Certificate of Merit is made up of BOB's, Group placings and Best in Show/Reserve Best in Show awards.
http://www.thekennelclub.org.uk/download/1753/scomform.pdf
whereas the Junior Warrant is made up of 1st placings at Championship shows or Open Shows. The only time a BOB counts is if you do not gain a point due to there not being enough in the class.
http://www.thekennelclub.org.uk/download/1752/jwform.pdf