Definitely stop doing the work manually.
If you just need to sync inventory across Shopify, Amazon and manually entered wholesale orders, use ShipHero FREE which is totally free. You can get ShipHero FREE at https://apps.shopify.com/shiphero-free
If you want to be able to cycle count your inventory - you can see a video about cycle counting at https://vimeo.com/103461524 - you can use the paid version of ShipHero, which you can get at https://apps.shopify.com/shiphero