My slight arranging and improvisational skills, be they what they may, came about from necessity. When I started playing the piano I did not play by ear and many of the songs that the pastor wanted to sing in church I could only find in lead sheet format. Or chord symbols above the lyrics.
My piano playing was touch and go in the beginning.  Many days I felt discourage, and what on earth did I think I was doing learning to play at the late great age of 27. My piano technique is still very far from perfect but adding my own touches here and there, working on left hand patterns (where I still struggle) and extended chords allowed me to basically become a pianist that has a very hard time playing only what is written. Meaning I improvise naturally.
Occasionally I feel like I’m cheating or something. Improvising is, as far as I’m concerned, much more fun that playing note for note. At those times I return to the basic and work playing as the arranger intended. I think it’s good for me.
But far from being a negative skills in piano improvisation have allowed me to have my own “sound” and to know what to add to change the sound of a song and help portray the message.
Recently reading over one of Greg Howlett’s articles, Introduction to arranging and improvising, I liked many of the points he touched on but most importantly his 6 steps for improvising or arranging a song. In step 2 he notes that after a while you will find yourself being drawn to a particular song. So true. For me as of late this has been Blessed Assurance. I’m drawn to this song and note myself adding suspended chords here and there along with working up an intro that has more of a gospel feel to it.
By the way the article, Introduction to arranging and improvising, in it’s entirety is a good read, as usual from Greg.  You will learn great tips for improvising your own songs.
Having a set number of songs that you have arranged and improvised on is a great idea for a church musician. You never know what situation will arise that your skills are needed. Although I know this takes time a fabulous idea would be, using the Topical Index or hymnal, arrange a song for each topic and keep a notebook of these for your own use. Definitely a long term project and not one to be entered into with haste.
Greg also mentions using the Nashville Numbering system. Roger Bennett Direct has a great instructional tape called just that Nashville Number System 101.