The perk you have to “chose” for the mechanist is the one making the hero count as mech (i.e. give hero the him/herself 50% mana at the start of each battle). The +5magic for brown weapon is an automatic bonus which should work as long as you have the mechanist lvl20 (for the max +5 bonus).
The easiest way to check it is: open your team editor (troop list), go to the weapon list - and find black manacles there. Check the dmg displayed ON THE LIST - this should show your weapon dmg w/o the hero bonus for specific color weapon. NOTE: you have to read the number from the list itself, the moment you CLICK on the weapon (Even w/o equipping it on the troop list in the team) it will already show the dmg boosted by your bonus. The dmg on the list should be 5 lower than when you click on it or equip it (for the Black Manacles).
If the dmg is the same, there are a few possible reasons:
- you didn’t lvl your mechanist (though that should still give +1 magic on lvl1 I think? might be wrong) - it actually happened to someone I know, bit embarrassing but super easy to fix - you said you did that though,
- you did lvl your mechanist, but you didn’t activate the mechanist class, and are using different class (That’s why mechanist magic bonus doesn’t apply to your manacles) - that’s also something you’d notice if you play the bombot team ;),
- if you checked all of the above - it actually might be some kind of a bug, in which case -> https://gemsofwar.zendesk.com/hc/en-us/requests/new
For me it works as intended (just checked it in case it was a general issue).