Shipstation
I have a separate login for my employees and I can assign specific shipments to them (the ones that I'm self fulfilling) and I don't assign them anything that will be fulfilled via Amazon Multi Channel Fulfillment. This last extra feature costs an extra $5 a month but it saves a lot of confusion and stress. It used to be that everything was under one login and they would fulfill all the orders even ones I didn't want them to fulfill. Good problems that they are responsible but a big fail.
The first 50 shipments a month are $9 and then after that it goes up to $29 a month. I rarely get to the $29 a month range because most of my self fulfillment are through Amazon multi channel and those don't count towards your allotted 50 even though you can add the tracking to shipstation and it will update to the marketplace.
Stamps.com
Keep in mind that if you purchase shipping through Amazon (and I think eBay) they will also provide you with first class mail rates for no extra charge (not available for seller fulfilled prime) but that won't help for non Amazon (or eBay) orders and shipstation just puts everything in one place. Also if you purchase directly through Amazon it usually helps you win any A to Z cases.
Me Being Super Lazy!!!
You have to connect your shipstation account to stamps.com and then you can replenish funds directly from within shipstation.com. The problem was that I put the wrong credit card in stamps.com. I was charging my American express business platinum instead of business Gold so I was getting 1x Membership Rewards when for the same purchase I could have gotten 3x. It's only a few thousand in spending a year but why not!? I tried to log in to stamps.com and I couldn't remember my password. Then I couldn't remember my security answers! Then I got lazy, I left it on auto pilot since I'm allergic to phone calls. This was true even though I was keeping that card open just to pay for stamps.com replenishments! I couldn't get in to stamps.com and it was just easier to keep things the way they were. That's a $450 annual fee. That's criminally lazy.
Fast forward about a year later, I finally called up stamps.com today, and got my password reset and changed the credit card. About time!
Lesson of the story: Don't be lazy! Now, if I can just get myself to cancel the AMEX platinum...