the stamina value goes down but its supposed to happen when i press Q what do i do?

Your code formatted right looks like:

local stamina = 100
local user = game:GetService("UserInputService")
local Player = game:GetService("Players")
local player = game.Players.LocalPlayer
local Q = Enum.KeyCode.Q

local function IsQkeydown(Q)    
    return user:IsKeyDown(Q)
end 

local function Input(input, input)
    if not IsQkeydown(Q) then
        --nothing happens here
    else 
        if user:IsKeyDown(Q) and Q == Enum.KeyCode.Q then
            stamina = stamina - 10

            if  stamina <= 99 then    

                wait(5)
                while stamina <= 99 do
                    stamina = stamina + 10 
                    if stamina == 100 then 
                        --nothing happens here
                    end 
                end
            end
        end 
    end 
end

user.InputBegan:Connect(Input)

The main problem is how you use IsKeyDown. Ignoring other issues, the code calls to check if the Q button is held down and does it only once. What happens when they let go of it? The while loop doesn't even know when to stop (You code doesn't get there anyways).

Instead of doing that, you could use InputBegan and InputEnded in tandem to call the Input() function:

--Give proper names to services.
local UserInputService = game:GetService("UserInputService")
local Players = game:GetService("Players")

function onInput(inputObject, gameProccessed)
    if inputObject.UserInputState == Enum.UserInputState.Begin then
        --When a key is pressed
    elseif inputObject.UserInputState == Enum.UserInputState.End then
        --When a key is released
    end
end

UserInputService.InputBegan:Connect(onInput)
UserInputService.InputEnded:Connect(onInput)

Now we have the ability to see whenever a key is released. Right now this detects any key being clicked, like the mouse keys. To stop this we include a check for InputObject's KeyCode. We also need a switch which functions as the key being held (A bool type). We make it true when the Q is press and false when it's released.

local key = Enum.KeyCode.Q

local keyHeld = false

function onInput(inputObject, gameProccessed)
    if inputObject.UserInputState == Enum.UserInputState.Begin then
        if inputObject.KeyCode == key and not keyHeld then
            keyHeld = true
        end
    elseif inputObject.UserInputState == Enum.UserInputState.End then
        if inputObject.KeyCode == key and keyHeld then
            keyHeld = false
        end
    end
end

This is a simple way to make a on Key held mechanic. You can use :IsKeyDown but this way always stays within the onInput function. I believe the IsKeyDown method is put into some loop.

To test the final product I will use a while-loop to detect when keyHeld is ever true. If it is then it'll print something.

--Give proper names to services.
local UserInputService = game:GetService("UserInputService")
local Players = game:GetService("Players")

local key = Enum.KeyCode.Q

local keyHeld = false

function onInput(inputObject, gameProccessed)
    if inputObject.UserInputState == Enum.UserInputState.Begin then
        if inputObject.KeyCode == key and not keyHeld then
            keyHeld = true
        end
    elseif inputObject.UserInputState == Enum.UserInputState.End then
        if inputObject.KeyCode == key and keyHeld then
            keyHeld = false
        end
    end
end

UserInputService.InputBegan:Connect(onInput)
UserInputService.InputEnded:Connect(onInput)

--Example test you shouldn't keep:
while true do
    if keyHeld then
        print("Running!")
    end
    wait()
end

The last thing for you to do is to handle the stamina decreasing when it's held. Let me know if you've understood what I've given or if I missed something.