NOTE: When making reference to third party add-ons like the Simple Inventory found on Chapel's Custom Macros For Sugarcube-2 site it is important to include a link to the add-on so that the potential answer-er (or other readers) will know of which one you speak of, it is also a good idea to list any extensions (like Passage Containers) you are using so that they don't need to work that out themselves.
The generated HTML of the PassageFooter special passage is added directly to the end of that of the current Passage, there is no separator or wrapper around the footer's content. This means that it's parent is the .passage classed div. I suggest wrapping both of the span elements within a parent div element to separate them from their current parent.
<<if not tags().includes("nofooter")>>\
<div id="passage-footer">\
<span id="footer1"><b>Visible Items:</b> <<container>>
<b>Inventory:</b>
<<droplist>>
</span>\
<span id="footer2"><b>Other Stuff Here!</b>
</span>\
</div>\
<</if>>
The main issue with your example CSS is that you have given both of your span elements a width of 100% (of the parent element's width) which means they can't both fit on the same horizontal plane. I would suggest change them both to something like 49%.
(note: you can't use exactly 50% for both spans because of the horizontal space of the border, and any potential rounding error made by the web-browser's render-er when calculating 50% of the parents width in pixels.)
#footer1 {
float: left;
width: 49%;
margin: 20px 0px 10px 0px;
border: 1px solid #000000;
}
#footer2 {
float: left;
width: 49%;
margin: 20px 0px 10px 0px;
border: 1px solid #000000;
}