The details of this depend a lot on what they're allowed to try to do, what is appropriate for them to successfully do, and what it is that they're actually attempting to do. Say for example, someone wants to take a bolt-charged gauss handgun which in accordance to the balance of the world deals 2-harm when set-against the electromagnetic shielding they use for 1-armor. The the savvyhead wants to add a laser sight into the gun, but not a typical laser sight–he want to tie it into optic nerves of a specific user, so when that user picks up the gun they see a targeting system resting in one eye. (which may or may not allow him to pin-point his targets through walls his gun is clearly capable of punching through.)
Well, the player might be using this to explain why he wants an (ap) tag permanently added to his weapon, or maybe just a +1-harm to it in general. In this instance, since we've defined armor as something that isn't layer on the body and that the gun is clearly capable of rending its way through the walls... I would say that a targeting system wouldn't help a gun lock-on to a target to deal more harm or pierce more shielding. I would have offered something along the lines of the statement above in the parenthesis. I point this out because the first thing you have to watch for in these types of hi-teched settings is that you keep the fiction real. No matter if the guy is a savvyhead or a chopper, what's in the world should still make sense for the world. Make sure you and him agree on what makes sense.
As for your question. Using the above example and then as a MC looking at the workspace... I would pose something along these lines to him:
When you go into your workspace and dedicate yourself to making this cybertech weapon, you're going to need...
a few dedicated days to get the job done
and
you'll need to get enough techno-scrap to do it. You can buy the techno-scrap from Jimmy the fixer on 4th and long for a couple of barter, else you can try to keep it all secret by taking apart some other working cyber-thing you've got laying around, or know how to grab.
and
you'll need to get a cybernetic-doc to put the implants into the target optics, and tie that to the sensors of the completed gun.
or
you'll need to have life-support added to your workspace and a couple of helpers that know what they're doing.
The key to it is that you're using the stuff he wants as a level-up bonus. Its a narrative goal that involves making a thing, which ordinarily isn't very interactive. Your job is to make it interactive. The choices are about setting goals for him in the world that if he can get out there and reach, it puts him close to getting the thing he wants. So if you want him to mess around with a gang sitting on some type of electromagnetic generator from the old days of the cyberworld... and he wants to add some electronic crap to his workspace–then you can say, hey if you want some electronic stuff, you'll need to get this thing from them... I dont know how, but that's what you need to do. Then give a time frame, and maybe a cost, if its something big. Make those options give him the incentive to interact with the world, but not so much that its no longer fun for him to try, or that is takes so long its not worth it. Make every one of his actions have weight, make it matter. If he offers to give the gang all better weapons, maybe those better weapons make the gang too strong, and they become something of a problem for other factions, npcs, players, or hell, maybe they want their generator back afterwards.
If he wants a level 99 weapon, it better take forever (I WANT A NUKE). But maybe in the process of doing that, he's making nuclear power, organizing construction crews, adding a nuclear facility to his workspace, needs to set up the space by a river or water source, making chemical labs racking out drugs or meds for money, coming into contact with the big government trying to take it all away, pissing on a gang that's out roaming the streets, pushing the character into interaction with the party, or using this as a way to create interesting PC NPC PC triangles.
Award creative storytelling, make powergaming-mechanics that might jeopardize your story harder, or offer cooler more sensible possibilities. Use the workspace to tell them what they actually need, and who they need to mess with to get it. Dont give it to them until they do all the things they need to. Do not be afraid to make up workspace additions for a project that you didn't expect. They want a nuke? They need a Nuclear facility, they want a nuclear facility? they need a chemlab, a river, uranium, the ultra sensitive tech inside, etc. They want those? well, maybe they gotta take the land from someone else, mabe they need to rob a location, maybe they need to buy it from this other guy, or help an enemy do something that another player doesnt like. whatever. Dont be afraid to tell them they need to track all the workspace jobs they want to do, dont be afraid to have them cue up like 10 projects, and dont be afraid to tie those together in ways that make sense.
Just let them be awesome, make their lives interesting, and tell a story.