The former Pollok and Arthurlie striker is no stranger to Stair Park having spent three years at the club in a coaching capacity.
However, it was still a surprise to some people when he swapped Championship Dumbarton for a club bottom of Scottish League One.
Waddell said: "Once I knew Stevie Farrell was getting the job at Stranraer and we spoke about the feelings we both had for Stranraer and how well we work together, it was an easy choice.
"I wanted to keep working with Stevie but it was hard to leave Stevie Aitken as well.
"He brought me to the club originally and it has been five years, give or take, of working together.
"I think Stevie Aitken's path is going in a very different direction to ours.
"Stevie Aitken is destined to go full time and he deserves a crack at it and I really hope he gets it.
"I've got my job and that would not allow me to go full time.
"The decision to go with Stevie Farrell was a no brainer but to come back to Stranraer was an even bigger no brainer."
Waddell initially joined the Blues as Dexi Wingate's number two in charge of the under-19s more than four years ago.
However, when Wingate left, Waddell made the step up.
He said: "Then I moved up to the first team and we had two very good seasons.
"We some good cup runs and went to Ibrox and were unlucky not to get promotion to the Championship.
"Once you leave Stranraer, you always check for results and you have connections with players.
"The affection for the club never leaves and now I am just happy to be back again and hopefully we can take the club forward."
Waddell originally left Stranraer for a short spell as assistant manager at former side Arthurlie before he was reunited with Aitken and Farrell at the Sons.
Now, after successfully keeping Dumbarton in the Championship last year and leaving them well set to match that feat this time around, Waddell is facing a new challenge.
The Blues were bottom of the pile and looking at a return to Scottish League Two for the first time since 2012 when he returned to the club.
Since then, Farrell, Waddell and the rest of the backroom and playing staff have worked tirelessly to turn things round and leave Stranraer in a healthier position, although there is still work to be done.
He said: "We don't want to get the automatic relegation spot.
"If you are in the playoffs it is not something you want either because you know anything can happen."