In my opinion, how picky are you with regards to getting the Fender clean? Have you owned a good Fender tube amp before...do you know and love that tone from first-hand experience? If so, you're going to end up disappointed. I own a Mark IIC upgraded to a IIC+ *and* I own a Fender Deluxe Reverb Re-issue (DRRI). I've given up on trying to make the IIC+ sound like the DRRI.
Here are the challenges:
1) The Fender has a very different feeling to its bass and low-bass. It's not necessarily that the Fender has more bass or less bass, it's just that it feels different. I think that the Fender might extend to deeper frequencies, but doesn't have quite as much in the low mids. On the Boogie, be sure to pull the "bass shift" knob or pull the "pull gain". IMO, don't do both...you get too much low-mids.
2) The speaker in the boogie (assuming you have an EVM) and in the Fenders sound quite different. The EVM has more mids and upper mids. While that's super-great for lead work (either lead or clean), it changes the feel of the clean rhythm sound because it changes the relationship of lows to mids and of highs to mids. The speaker could be an important contributor to my feelings on the bass frequencies as discussed above. The ear gets very easily tricked by what's happening at other frequencies...so more mids from the EVM could easily give the perception of odd bass (see above) or odd treble (see below).
3) The high high treble on the Fender and Boogie feel quite a bit different. On the Fender, the "bright" switch on the Twin (it's permanently active in the DRRI) puts a nice sparkle on the clean rhythm playing. On the boogie, the frequency cutoff and intensity of the "pull bright" ends up not being the same (because of where we tend to run Volume 1 on the boogie). It just sounds different. Plus, the boogie has a presence knob whereas the Fenders don't. The presence is a kind of high-treble control, so it's shape will be different out of the boogie than in the Fender.
4) The Fender's reverb (if you're talking about the Twin or Deluxe, but not the bassman), the reverb is of a whole different class. The boogie reverb is too short and not as sweet. The Fender reverb is long and luscious and has a magical wetness when palm muting.
My overall suggestion, therefore, is to not try to clone the Fender sound. If you know the Fender sound and feel, you'll never recreate it on the Boogie. I would simply shoot for a good clean sound. There are several approaches. The most fender-like is to do something like:
Vol1: 6, pulled
Treb: 4-7
Bass: 4, pulled (very different for single-coil versus humbucker...turn down for humbuckers)
Mid: 3
Master: 2, not-pulled
Presence: 5-7
and here's the heretical bit: use the Graphic EQ to scoop the mids more. And to bring up some of the lowest lows and the highest highs. That'll get you some of that classic blackface Fender "mid scoop".
If you've got humbuckers, here's an alternate clean sound, which is much more compressed
Vol1: 10, pulled (though, at 10, the pull bright doesn't actually do anything)
Treb: 3-4
Bass: 0-1, not-pulled
Mid: 3-4
Master: 2, not-uplled
Presence: 5-7
Graphic EQ off.
Chip