Clockwerk excels in ganking and punishing enemies who are out of position. This is the key to Early and Mid game Clockwerk.
What is your skillbuild? I'm assuming you're maxing Rocket Flare in order to harass and get last hits. This is suboptimal, imo, for a number of reasons: It pushes the lane, uses a lot of mana, deals less damage than Battery Assault.
Battery Assault is Clockwerk's main damage dealing, ganking spell. Over a full duration, a max level battery assault does 1200 (not including magic resist) damage. Compare this to the 200 damage of Rocket Flare which deals a maximum of 1000 if you hit 5 enemy heroes with it.
Clockwerk is not a carry, you do not need farm, regardless of if you are middle or offlane. You get your Hookshot, Brown Boots, a Bottle, start building your blademail and you're ready to go roam. When you begin roaming, inform your team that the middle lane is open for farm so that someone can rotate to get the gold and xp.
Clockwerk does just fine with levels. Because he only needs level 6, and minimal farm he is usually put in the offlane where he can soak up xp and pester the enemy lane with power cogs.
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Offlane is great, but only if you can solo it. I always have a difficult time with Clockwerk in a dual lane. If you see that your team has someone jungling, try out the offlane.
Phase boots is good if you're getting a lot of last hits and winning the lane. Imo, Power Treads are far superior, especially if you take the time to tread switch when casting your abilities. This will stretch your mana pool, allowing your bottle to refill more HP and mana, effectively allow you to cast more spells between runes. Switch to INT, pop Battery Assault, and kill a jungle camp. Staying off the map can pressure the enemy team because they don't want to get ganked by Clockwerk.
Clockwerk starts to fall off later on, at least in my experience. I'm able to do a lot until the 30-40 minute mark, and then I start to struggle to make plays with little or no follow up from my team. At that point in the game its up to your carries to take over.
I am not a pudge player, so I cannot compare the two.
The way that you deal with a hero hiding behind his team is to flank around and get a better angle. Don't just sit in the lane and hope for a good opportunity. Create a good opportunity by moving yourself. Move into the fog, hide in trees, make it easy to Hookshot the hero you really want.
Clockwerk, same as other gankers and gap closers, are good against split pushers. They can jump out of the trees, onto the pusher and kill them. Sometime you may need someone to help you, others you'll be able to solo kill. Learn your limits with Clockwerk.
Dotabuff I am 2.6k MMR, with almost 150 Clockwerk games and a win rate of 57%. If you link your dotabuff I can check your items and give you a little more feedback. Clockwerk games with item builds