For 'current' paperwork - that I'm still working on or need frequent access to - I use a metal desk top file with 12 slots (files slide in from the top). All are labeled by project, and/or 'to file', 'shred', 'action today', 'action this week', etc. You might want one or more files labeled 'Transport' or 'To Assistant' and place specific sub-files with relevant paperwork inside that main file. Then you might want to get a file box for neat & safe travel - take it with you and bring it back. In fact, the file box may be all you need, depending on how you work.

I'm sure you can do this, but I do reccommend spending a week or so really paying attention to how you work best (papers in sight nearby? or does that end up a mess?) and paying attention to what you really need (stop yourself when you first begin to look for something - the 1st place you look or reach for is probably the natural place to keep it).

When I moved to a new office my husband pointed out that the computer hutch and the U shaped office especially with light colored furniture is a secretarial layout, and not a current one either. He redesigned my layout so I have a large desk and a side table for my computer, & printer. His simple change of my not being surrounded by hutch, desk, etc. gives a real professional look to my office.
In back of my desk is a series of 2 drawer wood lateral files which are counter height so I can put a plant there but also current files. I see a lot of clients so I needed space for their chairs. My clients can look out the window in back of me. I promise to take photos, but we moved into our house today, and I couldn't find anything until morning.
So we started with:
whats in your office that could go elsewhere>? Are you storing closed files? supplies, a printer (if a network is available)
What do you have that your assistant could have besides paperwork. He helped me utilize my assistant of 23 years better and redesigned her workspace. Ladynimue's suggestions about really paying attention to how you work best (and put the times down as well) are great. My observation of accts offices is they have every file in the building on their floor. I once saw a cartoon that said "the acctg dept is limited to having 100 files on the floor next to each desk"
You are an executive--they don't expect you to use the same furniture--ask very matter of factly what your budget is for new furniture, or better yet maybe they have some furniture stored someplace. Never hurts to ask.
The other thing I would do is take a look at every acctg persons office, or read the furniture mags until you see a layout that you might like. Maybe a friend can point you in a new direction also. I was really stubborn about wanting everything the way I had it before--because everyting was in reach & I complained that when I was on the phone that was a problem. We got wireless headsets. problem solved.
My husband is not an office designer--he runs his own company. His layout is very different. He has a rolltop desk that faces out so all you see is the back of the desk, and not the papers, inside. He has a work area to the left and to the right. They aren't connected.
He has a couch and coffee table in his office.

Remember when people said that computers would make offices paperless? LOL Didn't happen, did it?

Most of my work involves ongoing data analysis reports and projects that can take months to complete. Each report/project goes in it's own folder, secured by a rubber band (sometimes the folder is quite thick).

The date the report needs to be updated goes on the calendar. The folder goes in the file drawer.

I have a personal rule that the desktop must be clear at the end of every day. So, yes, use the files AND put them away in a drawer or a file rack.

In addition, don't move all the piles of stuff you have now to the new location. Clean out/sort BEFORE you move so you can start with a clean slate.

The clear desk at the end of the day rule is paramount for me, too. What I usually do is clear my desk and put things away while my computer is shutting down.

For hard copy materials, I'm not a big file folder person. For me, papers become too-easily separated from their folders, plus when I put papers into a drawer or a filing cabinet, they end up taking up space into infinity. I never seem to get around to culling outdated files when they're in a drawer.

My system is more bookcase-oriented. Projects with a lot of papers go into labeled binders. Projects with fewer pages or odd pieces (like booklets, CD-ROMs, etc.) go into labeled magazine holders. I put the project name, project lead, season, and year on the labels.

Current projects go onto the bookcase and shelves I can reach most easily when sitting at my desk. Older projects that I still need to hang onto go onto another bookcase or onto the harder-to-reach shelves. And when I run out of room, it's easy to look at the existing files and think, "I don't need that thing from Spring, 2005 anymore," and make room by recycling one binder or emptying one magazine holder.

I have to admit that the two-office thing sounds like it would be a major nuisance to me. I don't know if this would work for you, but I think if I were in that situation, I would really think about ways to control not just my space but my time. If you can compartmentalize your work time enough, you may not need to haul quite so much paper back and forth. For me, the main challenge there would be setting expectations, so that people understood that when I was in Office A, I wouldn't be working on Work B, but that it was on the list for when I was back in Office B again. In some office cultures, you can do that-- in others, I imagine it might be untenable. You probably know your own situation well enough to have a good sense of what would and wouldn't work in your setting.