Reverse charge is one of those things you really need to understand before doing B2B cross border sales. You should probably do more research before you continue. Some of the city handelskammer websites have good information, but if you're not sure, you should ask for professional help. I am not a professional, so do not take my opinions as fact.
You need a VAT ID for your business. The one that starts with DE, and it has to be on your invoice. Not simply a German tax number.
A B2B customer can ask you for zero VAT on a sale, but it's up to you to determine if they're qualified to receive it. You have to verify that their VAT ID is valid, by checking it on the official German verification website against the customers address, and (very important) you have to request a copy of the verification by pressing the button at the bottom of the page (after verification) and they will send you a paper by post which you have to keep for your records. It will say A, A, A, A, A if it's correct. If you can't verify the ID, then don't sell for zero VAT, or else you become liable for paying the VAT if you're caught not collecting VAT.
There is a difference between intra-community delivery and intra-community services. The difference is very important for B2C sales, especially electronic services because of the MOSS mini one stop shop for charging and paying VAT to the country in which the customer resides. Similarly, if you pass the minimum threshold for sales to a single country, even if it's not electronic services, you have to start charging the VAT rate of that country and send the VAT to that country's tax office.
However, assuming that you don't sell B2C to other EU countries, and you only sell B2B to other EU countries, then you can use the reverse charge procedure without having to worry about MOSS or the minimum threshold for sales to other countries, as those rules usually apply to B2C.
So after you have your VAT ID, verified your customer's VAT ID and address, you could possibly invoice with zero VAT. Assuming everything else about your invoice is correct, you also have to add a certain text to the invoice to indicate reverse charge. I've seen some sites that say you have to quote the actual tax code, while other sites say you only need to write intra-community reverse charge delivery or intra-community reverse charge services. (Edit: you also have to write your VAT ID, and the customer's VAT ID on the invoice.) Then if you are sending a physical product, you have to ship it only to the address that you used to verify the VAT ID. I've been told by a couple of accountants to not ship to an alternate address, because you won't be able to prove that the zero VAT sales was delivered to the intended company for business use. So if a customer demands zero VAT and shipping to a different address, I simply don't sell it, unless the customer is willing to pay VAT, or agrees to take delivery at the registered address.
After delivery, you have to keep a record of the waybill and a delivery confirmation showing the delivery address, like a printout of the shipping label and tracking records from the shipping company, along with the VAT ID verification that you got in the post, and the invoice that indicates reverse charge. The delivery confirmation is something that is still unclear to me. I think it used to be that you had to get the customer to sign a statement declaring that they received the delivery and that it was intended for business use. But I think the rule was changed, so that a printout of the tracking was sufficient. But I'm not sure and you should look for official sources of information about this requirement.
For the monthly VAT forms, assuming that I sell "standard" products and not special products or other special situations, there is a separate box for entering zero VAT delivery sales, and a different box for entering zero VAT service sales. I usually put mine in box 41 and 21.
Zero VAT export outside of the EU, I put in box 45.
If I buy something from B2B, as my own business expense, and it was sold to me with reverse charge, then I charge myself VAT and then immediately refund it to myself, in boxes 89 (for 19%), 61, and 46, 47, 67.
The annual forms have similar boxes, but are numbered differently.
But it will be different if you are selling special products and services, like minerals, food, vehicles, property, assets, business, triangular sales, pass through sales, etc.