Mixing up the track types on a regular basis might be a bit strange, though... And mixing those two particular track types is not as easy as it looks. Code 55 is the nice-looking rail, as opposed to code 80. The code refers to the rail height in thousandths of an inch -- 0.055" or 0.080". In correct scale, rail should be between about 40 and 55 (smaller for branch and yard track, over 50 for big main lines). That's why code 55 looks good whereas by comparison code 80 looks very oversized. Again, depends on how picky you are...
The trouble comes with the two types... Atlas code 55 rail is 0.055" high, and has plastic moulded bits in the ties that hold the rail on (of course). By necessity these are quite high, and can interfere with cheaper and older wheels that have large flanges intended for use on code 80 track.
Peco code 55 uses a special type of rail, actually 0.080 high but set into the plastic by 0.025", so only 0.055 of it is above the ties and visible. This makes it not only stronger, but also the 'chairs' (or whatever you want to call the bits that connect the rails to the ties in real life) are not actually holding the rail to the ties -- they're just for show and are therefore much smaller. For this reason even well-oversized flanges as found on old and cheaper locos and rollling stock will work happily on Peco track. It is quite handy if you also have Peco code 80 track for inside tunnels and staging yards, because it connects without trouble to code 80 track and the rails are at the same height. The same applies to Peco 55 or Peco 80 and Atlas 80.
Atlas 55, however, is lower overall than these three, and as such connecting Atlas code 55 to Peco code 55 is a little tricky -- you can't just slide on a joiner. You can file off the lower flange from the Peco and join the two together, or you can put a joiner on the Peco track and then just sit the Atlas on top of the joiner and solder it there, so it's possible although not ideal.
I still think the biggest problem will be that the junction from Atlas to Peco will look daft, as the ties are different. I would suggest either sticking to Atlas 55 on its own, or going with Peco code 55 and then you can use Peco 80 (sometimes cheaper, and available secondhand on ebay) for tunnels and hidden areas if you want to save a few quid.
Mind you, it's nothing in the scheme of how much you're going to end up spending on the whole layout so you might just want to bite the bullet and then forget the bill. That's what I did!

))
Charles