Andy McCoy's two goals rewarded Linnets fans who again headed for Wincham Park - some of them on foot.
The sponsored walkers went the extra mile by trekking from the breakaway fans club's spiritual home in Canal Street to the newcomer's temporary base in Northwich.
Their efforts are expected to raise about £1,000 for the fledgling club.
Bootle, having already drawn at home with Runcorn in the league and beaten them in the Division Two Cup, were again difficult to break down but less of a threat up front.
But they effectively pressed self-destruct in first-half stoppage time.
Jack Flood, having already been booked for dissent in kicking the ball against the pitch fencing, talked himself into an early bath.
Runcorn looked to have capitalised before the interval but Dave Thompson's cushioned header from Colin Flood's cross from the right was ruled offside.
However, Thompson, Paul Scott and in the second 45 minutes Michael Young caused no end of problems with their pace and quick thinking.
The trio combined for McCoy to fire Runcorn ahead at the far right post in the 54th minute and the same player made sure with a rasping finish three minutes from time after Young had again made ground on the left.
Although well-drilled and typically competitive, Bootle played with only one up front even with a full complement and had just one worthwhile shot in the game.
Linnets' second might have been scored earlier but sub Colin Quirk's 62nd-minute effort from 30-plus yards came back off the bar and Paul Scott's 70th-minute humdinger from eight yards outside the box forced a to save from Mark Mawdsley.
Linnets: Holcroft, Holmes, Flood (Parle 90), O'Driscoll, Boden, Edwards (Quirk 28), McCoy, Scott, Thompson, Loughlin, Young. Referee: C Thompson. Attendance: 200.