The SRU announced the scheme which they hope will ensure players on the fringes of the Glasgow and Edinburgh teams are playing regular competitive rugby.
While some players at Glasgow and Edinburgh have previously had ties to Premier One teams, the SRU's new project means all 72 professionals now have second clubs.
Many are unlikely to have any playing duties with the clubs to which they are now affiliated, including Scotland captain Mike Blair who has been drafted by Edinburgh Accies.
However SRU chiefs, who have discussed the move with Edinburgh head coach Andy Robinson and his Glasgow counterpart Sean Lineen, believe the Scottish game can benefit at all levels by creating the link-up.
Glasgow Warriors assistant coach, Shade Munro, said: "The clubs have played a massive part in helping the professional players get to where they are today, so this is a great opportunity for the players to give something back.
"The pro-team players receive coaching and advice every day - from specific rugby skills to nutrition - so hopefully they can pass on their knowledge through their allocated clubs and help the development of the new generation of professional players."
Selkirk, who gained promotion as runners-up in Division Two last season, had the first pick in each round of the player draft, and Division One champions Boroughmuir were last to pick.
Each team selected six players over the course of the draft.
The SRU's head of community rugby Colin Thomson said: "We all want to see players playing.
"Clearly not all professional players will play for the Premier 1 club to which they have been allocated during the season as they will have commitments to their pro-team and potentially international obligations too.
"But this agreement means that some professional players who are on the fringe of selection for their pro-teams get the opportunity to play and share their experiences from the professional tier with some of the best players in the community game and this is being seen as a positive step for Scottish Rugby."
Teams will face restrictions in the number of allocated players they can pick, with a bar on fielding any more than two additional professionals than the opposition select in their squad.
Player allocation:
Selkirk: Sean Crombie, Simon Cross, Ben Meyer, Gavin Kerr, Ross Ford, Phil Godman.
West of Scotland: Jon Welsh, Richie Vernon, Colin Gregor, Andrew Henderson, Fergus Thomson, John Beattie.
Edinburgh Accies: David Blair, Greig Laidlaw, Hefin O'Hare, Mike Blair, Hugo Southwell, Ben Gissing.
Glasgow Hawks: Eric Milligan, Colin Shaw, Steve Swindall, Max Evans, Graeme Morrison, Thom Evans.
Hawick: Matt Dey, Opeta Palepoi, Calum Macrae, Chris Paterson, Matt Mustchin, Dan Parks.
Stirling County: Ryan Grant, John Houston, Roland Reid, Allister Hogg, Alastair Kellock, Mark McMillan.
Heriot's: Jim Thompson, Steven Turnbull, Alan MacDonald, Nick De Luca, Ross Rennie, Bernardo Stortoni.
Ayr: Calum Forrester, James Eddie, Ruaridh Jackson, Moray Low, Sam Pinder, Lome Fa'atau.
Currie: Andrew Easson, Andrew Turnbull, Dan Turner, Ben Cairns, Simon Webster, Dougie Hall.
Melrose: Scott Newlands, Geoff Cross, Mark Robertson, Kelly Brown, Kevin Tkachuk, Tim Barker.
Watsonians: Kyle Traynor, Craig Hamilton, A Kelly, Daryl Gibson, Jim Hamilton, John Barclay.
Boroughmuir: Steven Lawrie, Fraser McKenzie, Ed Kalman, Allan Jacobsen, Dave Callam, Justin Va'a.