One thing I've found helpful when I don't use a subwoofer is this: in the amp block, engage the Bass Cut switch, and then regain some of the low end back (to taste) using one or more of the following: Bass (tone knob) parameter; Depth (pg. 2); Graphic EQ; Thunk. Also depending on the IR you are using in the Cab Block, the proximity, mic selection, and the Speaker Drive can all be used to shape the tone a bit.
Compression is also a big part of taming the beast, as karmakarmakarma has mentioned. You can also mess with the amp block Compression parameter (+/- noon setting) as well as the dynamics parameter (noon +/-), or any of the compressor blocks in the Axefx. Compression is tricky, though, and a topic all to itself. Unless you're really good already at understanding compression, you may want to take your time in that department. There are some decent bass compressor stomps (hardware) out there, and I'm hoping to see one of these modeled at some point, just to streamline the process of getting settings more easily. Much of the time I'll put a front end Pedal 2 comp, with slow attack, fast release, and sustain set below 1.00, and with emphasis on around noon. Multiband Comp is cool, but it can be tricky setting it so that the bass doesn't completely go away. IIRC, the low band frequency bottoms out at 120hz, which IMHO is a bit too high for my liking for the purpose of eliminating speaker flub... been wishing they'd broaden the sweep on both bands a bit, to help out bassists a little more...I digress.
It really is a fine balancing act unless you are using a FRFR cabinet that is properly designed to handle such low end, or without adding a sub. One of my arsenal of full range cabinets is loaded with a 15" high power handling coaxial (Ciare, passive, bi-amp only), loaded into a bona fide bass guitar cabinet. Tons of low end (sometimes too much, if you can believe it, especially in the back of the room). However, this cabinet is the furthest thing from flat response, but it's a helluva loud rig that is relatively compact (I've got 2 of these cabs). And being a bass cabinet, it really does retain a lot of traditional bass cabinet feel, compared to regular powered PA tops and subs. They weren't inexpensive, either. FWIW.