Main was sent off minutes after heading home a stunning winner against Neil Warnock's team a week ago and is available again after serving a one-match ban.
"He's going to travel, he's done well and come back with two goals and it's important we utilise that confidence factor," said manager Tony Mowbray.
"He's been out a long time and sometimes players burst back onto the scene and then the adrenalin wears off. We'll use him as best we can and hopefully when he comes on he'll score some goals."
England U17 skipper Morris, who became Boro's third youngest player of all time when he made his debut against Hastings last month, will travel to Lancashire as Mowbray struggles to find 18 fit players.
Stuart Parnaby will be missing for four-to-six weeks with a hamstring tear, compounding the continued absence of the club's only other specialist right-back Justin Hoyte.
"That's a disappointment on the back of Hoyte being out and is going to leave us short," said Mowbray.
Lukas Jutkieiwicz and Josh McEachran both went over on their ankles during the game and will be assessed.
Centre-halves Seb Hines and Jonathan Woodgate are still out, raising the possibility of Stephen McManus making a return to the starting line-up.
"Stephen's a top professional footballer and he's learned his trade at a top club in Scotland," said Mowbray. "I've got no doubts whatever about Stephen if gets asked to play."
Top scorer Scott McDonald is also ruled out, although he is described as being "touch and go" for the weekend game against Millwall.
"He's been training with the physios on the grass but he's still feeling it (his back) a bit," said Mowbray.
Despite the injury situation, Mowbray - who says he is not looking towards the loan market at this stage - retains faith in his fit players to get the season back on track.
"I try not to make excuses even though we're a long way from a fully fit squad," he said. "Yet in the first half of the season we were in the same position and we continued to win matches and I sat here talking about the strength and depth of the squad."
Despite their recent slump, Boro are still four points clear of seventh-placed Brighton and tonight is a welcome opportunity to put Saturday's nightmare at Crystal Palace behind them and claim a first away win since early December.
"We know people had paid hard-earned money to go a long way at the weekend," said Mowbray. "But there's no lack of desire or effort from the team.
"We're being punished for pretty basic mistakes which we didn't make for the first half of the season. We have to work our way through it.
"It's incredible after the run we've been on that we still find ourselves in the top six and in the fifth round of the FA Cup but we have to start winning football matches.
"I've said to the players I'm pretty confident we will. If we don't make the top two hopefully we'll make the top six. I'm pretty sure we'll finish with a strong run, hopefully starting tonight.
"The mood is still positive. I tried to give them an analogy about a boxer getting back up and throwing the first punch again and I'm sure we'll do that and that at the end of the season we'll be looking back on a sticky period in January and February."
"Burnley are very hardworking and honest and like Crystal Palace have a centre-forward who has scored a lot of their goals in Charlie Austin.
"You know where their main threat is, as we did on Saturday and yet were unable to stop Glenn Murray scoring twice.
"But we've gone there in the past and won and that has to be the aim again. We need to go there and be more resilient than we've been and work extremely hard."
The Clarets are without defenders Ben Mee (knee) and Michael Duff (calf) but Sam Vokes is hoping to be involved despite injuring his foot after scoring twice for the reserves against Stoke last Tuesday.