The Nelson Mandela University side spent two years in the Varsity Cup – the highest tier of the competition – but finished bottom of the combined log over those seasons to be relegated to the Shield tournament for 2023.
Manuel came in as the coach in November last year with the mandate to rebuild the system at the varsity.
Although they were disappointed at being relegated, he said it was important to face the reality of the situation.
"Rebuilding the system needs time and the objective is to create a legacy here that will outlast me and that will be a lighthouse for the next generation of student-athletes," he said.
With his first Varsity Cup season as Madibaz mentor now behind him, Manuel underlined the value of experience.
"We competed with a very young team who had not played at this level before and we have to get games under their belt and get them to win more to grow belief," he said.
"We are busy with our recruitment strategy to ensure we can get players who add value to our system. It is also important to establish a pipeline from our schooling system in Gqeberha."
Manuel acknowledged that moving to the Shield competition would complicate the recruitment process, but said he was already in conversation with the current squad to assess their plans for next year.
"We would like to keep 90 per cent of this squad to maintain momentum and build experience. We are aware of the challenges and that we need to find ways to work around it."
The Madibaz mentor said one of the biggest factors was to bolster their personnel up front.
"You need a more experienced tight five to manage the demands at Varsity Cup level," he said. "If you don't have a competitive set piece, you will struggle.
"Players need to improve technically right across the board in terms of generic and positional skills, so there is a massive amount of work ahead of us."
Despite the challenges they faced, Manuel praised the squad for the fight they showed each week.
"We had our first win in two years (against Central University of Technology) and our game against UCT in Cape Town (lost 33-26) was close.
"I felt that [the match against UCT] was the tipping point. If we had won that one it could have led to a better finish to our campaign.
"Although disappointed, the positive is that we can use the remainder of the year to build and develop the system and our players, to beef up our tight five and to establish a winning culture."
Manuel thanked the Madibaz fans for their support.
"They have been great. There is truth in the saying 'Rome was not built in a day' and I believe the supporters have seen some improvement.
"It's now a matter of being patient and placing trust in the fact that we are busy with a process to build a better rugby programme that will serve the generations to come."