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The best depends on your particular usage and types of content. And
whether you have a CF slot SD slot or both. I think the X5 has both?
Keep all system dependent files in the PPC internal memory. This is
critical. Anything that is needed at startup, Today plugins, cardfile
formatter,encryption program, activesynced files, and other common
essential utilities. I then have an SD card for most games,large non
essential programs and some media content. A CF card with an MP3 player
and current MP3 favorites. Another CF card with a navigation program and
all the charts for the voyages. A combo Wireless CF card with memory so
I put some of the programs that *require* 802.11b access on that card.
The fastest way to transfer a lot of files from a PC to a PPC is by
using a media card reader on your PC. Try to keep the number of programs
installed in the PPC internal memory to a minimum. This leaves more
memory for running applications or transferring large files if a card
reader is not available. It also keeps backup times through Active sync
to a minimum. All content on your external cards can be backed up to
your PC and most files swapped out via a media card reader. I use a
PCMCIA card reader which is very fast.

Most multimedia content can be transferred using a media card reader for
your PC. Not possible with some protected content, hence the reason I
use MP3's only for music. Most protected ebooks will also transfer via
media card reader and work as long as the associated PPC program is
registered for the same user as the PC's. Some protected content will
only allow for tranfer using the ActiveSync mechanism....I generally try
to stay away from such services and content unless they allow for a
means to convert the files. For example I use iTunes...burn the AC3's to
disk as a CD...and then rip them back as MP3's.If possible you want
large multimedia files that don't require synchronization with
ActiveSync on external cards. Activesync is slow and unreliable. There
are some third party sych addons that will sync to CF and SD cards also.
Card readers are fast,convenient, and cheap. I saw some great deals on
CF and SD cards during this holiday shopping period also. Hopefully even
cheaper after XMAS. With only a single card slot you can install what
programs you have and back up the card. Then you can restore to several
cards and  keep all or some these programs available on different cards
yet fill up the open space on each card with various content. This is a
great scheme for a single slot PPC for a music lover. You can fill the
remaining space on one or more cards with music, yet still have other
applications always available. And maybe another card with the same apps
and your digital picture album. All depends on what you use yours for,
how much content you have and want available and how many cards are in
your budget.

Make a plan that works for how you personally use your Axim. For someone
who doesn't have both CF and SD slots, or whether and which slot might
be used for a wireless card or other device, they will be more
restricted than having both so think up a scheme that best suits this.
Most people don't need such an extensive scheme. They may only use a
single card, or have a separate MP3 Player or whatever. Just some ideas
to help you figure out what you think may work best for your particular
usage and budget.

Specific to your second question...once again....get a media card reader
for your PC and try to stay away from protected nonconvertible media
types that won't allow for transfer via a media card reader.