of course you can now applique on your finished runner- i would have to wonder about the extra padding though....if you plan to actually use your runner on a table will you want to set anything on it? added padding will give it a very uneven surface- cause for items to tip over easily if placed on it --- but if it's just for show & will not be actually used where anything will be placed on it you could certainly do it that way ---your project do what you want---remember though- if you are using the extra padding you will need to cut your applique pieces with a larger than normal turn under allowance to make up for the batting.