HDD-CDROM-MOTHERBOARD

Hello this is Rahul Ghosh from Kolkata(India).
since last few weeks i.e. ever since i've installed
another harddisk-40GB with the existing previous 20GB, my
system has become a bit slower(taking more time to boot)..
I also have got 2 CD dirves installed in that system & I'm
running win-ME with win-XP as dual boot..
Whats the reason that my system has become slower than
before & whats the remedy to make it as fast as it was
earlier(ie. before installing the 40GB harddisk)???
Also I've noticed that working on one drive is
automatically consuming 40kb,80kb,120kb and likewise space
on other drives on subsequent booting(details given at the
bottom last ).. why is this so happening & how can it be
prevented???

Is it because that I'm having 2 harddisks connected as
primary master and primary slave and 2 CD drives connected
as secondary master and secondary slave ???
what is the generalised/correct rule of connection for
better functioning/result of the system if somebody has 2
harddisks and 2 CD drives in his system??? I mean to say
how should one connect the 2 harddisks & 2 CD drives with
the motherboard IDE ports in terms of primary & secondary
master/slave???

Details: My 20GB HD has got 3 partitions-C:, E:, F: and
the 40GB HD has got 3 partitions-D:, G:, H: ...
I'm having 2 operating systems as dual boot--win-ME is
installed on C: and win-XP is installed on D: ....
Now when i'm working on say E: or F: while using win-XP,
then it is found to automatically consume say 40kb or 80kb
diskspace on G: or H: when restarted in win-ME and vice
versa.. And this consumption of diskspace is getting
increased automatically on such activities after few
rebooting...
why is this so happening and what should be done to
prevent this and make the system work smooth & fast???
PLEASE HELP ...

Regards.
Rahul Ghosh..