Disclaimer: You know how this goes.
Thomas wasn't allowed into the lair till he turned sixteen, he knew about it of course. It was no secret what his parents did at nights, his father's self-appointed duty. It was something the family shared.
But their nightly activities were something that had, till now, existed in a parallel world to his own life. Wherein his parents were both hardworking and savvy business people, that despite what all the clichés insisted upon, always made time for his and his sister. In the parallel world his parents fought effectively for the future of what would hopefully be a safer city for their children. He was proud of his parents in both worlds.
Thomas was only able to step foot into the lair once he was old enough to begin to understand both the dangers and responsibilities of being a part of that world. Despite his newly allowed visiting hours in the lair, there was no way Thomas ever went into the field. His visiting hours were spent with whoever remained behind when a mission didn't demand the full strength of Team Arrow.
Uncle Diggle would train him in firearms. He was barred, of course, from firing off any live rounds. But Thomas could take a handgun apart, clean it and put it back together, blindfolded. They would often sit together listening to the comms, cleaning while Digg told war stories or Arrow adventures from their early years.
Uncle Roy taught him parkour whenever he stayed back to train. Thomas would help set up the obstacle course and then they'd both run drills. Of course it had been Oliver, who taught Roy, but Roy was smaller with a more agile frame and many years of training meant he was a great practical teacher. They'd run the course side by side, pausing when Roy showed Thomas a different technique or flip. Roy would often point out that in a different life, sometimes all he could do was run and that sometimes it was the only thing that saved him from a lot of pain.
His Mum taught him as much as he could understand about the technology side of the operation, but her computers in the lair remained untouched, save for the regular cleaning undertaken by Diggle on Felicity's strict instruction and were remotely updated by Felicity herself. She refused to visit the lair while Maddie was still young; mostly she monitored operations from her home office.
She was intent on being every single bit the parent her own mother never was. Thomas could attest to her success in this, he'd only met grandma once. He had to call her auntie. Felicity was her polar opposite, Oliver even agreed to her decision (although Thomas thinks his Dad agreed so easily because it means Mum won't argue her way into fieldwork as much). Her passions shone through during every lesson; truthfully she'd prefer her son to sit behind a computer than be out on the street, if his field ban was ever lifted.
Thomas rarely trained with his dad though. It was tedious and boring. He was also confused when one day in the middle of such a rare session, Roy walked into the basement and taking in Thomas and his "training" a look of nostalgia passed over Roy's face, which was promptly cracked in the middle by a secret smile.
Surely Roy didn't miss training that much.
His dad only ever made his slap bowls of water.