The Rovers boss expects Chris Powell's Addicks to set up in a similar way to Huddersfield Town when the two sides met last month.
However, backed by a strong and vocal home support, Bowyer is confident that Rovers can get all three points to continue their decent home form.
"Obviously teams will now be coming to try and set up to stop us playing and frustrate us, a little like Huddersfield," said the manager.
"That challenge for us is to be patient and to try and break them down. It is something that we have spoke about this week with the players.
"People are going to be looking at ways to stop us, looking at how we play and how they can counter that. So we've be discussed being patient, about not getting frustrated, and we'd appeal to the fans to have the same mindset.
"If it means we score in the last minute and win 1-0 then we'd be delighted with that.
"Against Watford the fans were superb for us and certainly helped us get over the line in that one.
"It is a game of patience and if we can get on the front foot early and get an early goal then that changes the complex of the game.
"Performance wise, both home and away, have been similar, but our home form results wise has been really pleasing for us.
"We want the opposition to know that they are going to be in for a very tough afternoon, and backed with the atmosphere the fans have created in the home games so far the two go hand in hand. So hopefully we can keep working on that."
Tickets for Saturday's match will be on sale until the 3.00pm kick-off. Prices are from £15 Adults, £10 Seniors and £5 Juniors. Book online today at www.onerovers.co.uk
and collect your tickets from the Blackburn End collection point on the day of the game.